################################### ## BMRB Data Deposition Form ## ## Version 2.1 ## ################################### ################## # Introduction # ################## ################################################# # Where to submit a completed deposition form # ################################################# A completed form, as an ASCII file, can be submitted by anonymous ftp. Submissions that contain non-ASCII data will not be recognized. Anonymous ftp - ftp.bmrb.wisc.edu Place files in the '/incoming/data_submission' directory. Once the files are submitted, they can only be manipulated by BMRB staff. Please notify Eldon Ulrich by email at elu@bmrb.wisc.edu ####################################################################### # Where to obtain answers to questions concerning the deposition form # ####################################################################### Detailed instructions for completing the form- URL: http://www.bmrb.wisc.edu/depform.ins - Anonymous ftp ftp.bmrb.wisc.edu Directory: '/dep_form' Filename: 'instruct.frm' Sample deposition forms - URL: http://www.bmrb.wisc.edu/elec_dep/example.frm - Anonymous ftp: ftp.bmrb.wisc.edu Directory: '/pub/dep_form' Filename: 'example.frm' Atom nomenclature - URL: http://www.bmrb.wisc.edu/Nomenclature/commonaa.html List of ligands, cofactors, etc. - URL: http://www.bmrb.wisc.edu/elec_dep/molecules.html Contact - Eldon Ulrich Tel: (608) 265-5741 FAX: (608) 262-3453 Email: elu@bmrb.wisc.edu ######################### # The Deposition Form # ######################### data_ # The accession number will be provided # by BMRB. ########################### # 1. Entry information # ########################### # The entry identifiers are used to provide a short title and a # minimal description of the information contained in each form that # is deposited. Each deposition represents data for a single biological # system. The system may contain more than one macromolecule (e.g., a protein # DNA complex), but studies involving multiple unique macromolecules, for # example a group of single amino acid mutants of one protein will require a # deposition for each of the biopolymers. A brief descriptive title is useful. # Something like "Lysozyme chemical shift assignments" is appropriate. # If the author wants to provide additional information about the # submission in the form of text, the '_Details' tag can be used. # The '@' symbols in the form are place holders indicating where data # values for data tags can be entered. The '@' symbol must be deleted if a # data value is entered for a data tag. Simply leave the '@' symbol where # data are unavailable, if categories are not applicable to your deposition, # or if BMRB is to supply these data. save_entry_information _Saveframe_category entry_information _Entry_title # MANDATORY (descriptive title # equivalent to the title of a # journal article) ; @ ; # If the authors for this entry differ from those for the primary # citation for the entry, use the following loop to list the authors. loop_ # Optional LOOP # Iterate once for each author _Author_ordinal # Integer value indicating # the order of the author's name # in the citation. _Author_family_name _Author_given_name # Please provide the full given # name (excluding the family # name). First initials are acceptable # only if that is the form of your name # that you use for publications. _Author_middle_initials # Provide initials only for # names not previously entered. A full # middle name can be entered, if that is # the form of your name that you use for # publications. _Author_family_title # [e.g.: Sr.; Jr.; III; others] Do not # professional titles. # # Author Family Given Initials Title # Ordinal Name Name # # ( 1 Doe John L.G. Sr. Example ) #----------------------------------------------------------------- # @ @ @ @ @ stop_ _Entry_type # MANDATORY [e.g.: new; revised; @ # supplement] _Entry_origination # Supplied by BMRB [e.g.: author; BMRB # PDB; NDB] @ _NMR_STAR_version 2.1 _Experimental_method # [e.g.: NMR; @ # 'stopped-flow kinetics'; # 'mass spectrometry'; # 'x-ray crystallography'; # 'theoretical calculation'] _Details # Optional (additional text ; # information) @ ; _Special_processing_instructions # Text description of any # special handling that will be # needed in processing this ; # submission. @ ; loop_ _Entry_ID_preference_PDB # IF this entry contains data that # will be submitted to PDB, PDB # allows authors to request up to # three ID codes. [e.g.: 1fey; 1fty; # 1ytp] @ stop_ # If the data in this submission depend on, extend, or are related to results # reported in existing BMRB entries, please enter the BMRB accession numbers # for those entries (e.g. an order parameter entry that depends on chemical # shift assignments in an earlier BMRB entry). loop_ _Related_BMRB_accession_number _Relationship # Text describing the relationship # between this entry and the listed # BMRB entry. @ @ stop_ # If this submission is a revision of a current BMRB entry, the BMRB # accession number for the older entry in the BMRB database must be # provided as a value for the data tag '_Revised_BMRB_accession_number'. _Revised_BMRB_accession_number # Accession code for the older @ # BMRB entry obtained from # BMRB via the WWW or anonymous # ftp. Addresses are given at # the top of this form. _Replace_BMRB_accession_number # Provide the accession_number @ # for the BMRB entry that is to # be deleted. _Revised_PDB_accession_number # For revised entries containing @ # atomic coordinates, provide the PDB # accession_number of the pertinent # entry. _Replace_PDB_accession_number # For revised entries containing @ # atomic coordinates, provide the PDB # accession_number of the pertinent # entry. _Revision_details # Provide a brief explanation # for the submission of this # revised or replacement entry. ; @ ; _Release_immediately # Optional: [e.g.: yes; no] @ _Release_on_publication # Default: [e.g.: yes] @ _Release_date_request # Optional: [e.g.: Year-Mo-Day] @ # Release may be delayed by # request for a period of up to # (but no more than) one year. _Release_date_justification # Cond-Mandatory: Provide a brief # justification for the extended hold # request (beyond publication). ; @ ; # PDB allows authors to define separate release dates for experimental # data and atomic coordinates. The following data tags are available # for authors depositing atomic coordinates that will be listed in PDB # to specify these release dates. _Experimental_release_date # Optional @ _Experimental_release_on_publication # Optional @ _Coordinates_release_date # Optional @ _Coordinates_release_on_publication # Optional [e.g.: yes] @ save_ ######################### # 2. Contact persons # ######################### # The name of one contact person is required for each submission. Including # the name of a second contact person is useful. The information requested in # this section will not be released to the public. The information is needed # so that BMRB staff will know whom to reach if questions arise during the # processing of the submission. save_contact_persons # MANDATORY SAVE FRAME # (use all data tags that apply) _Saveframe_category contact_persons loop_ _Family_name # MANDATORY (a name, even if it # is a single character, must be # entered for this data tag) _Given_name # Please provide the full given # name (excluding the family # name). First initials are acceptable # only if that is the form of your name # that you use for publications. _Middle_initials # Provide initials only for # names not previously entered. A full # middle name can be entered, if that is # the form of your name that you use for # publications. _Family_title # [e.g.: Sr.; Jr.; III; others] _Department_and_Institution # MANDATORY (a complete mailing # address is required in case BMRB # staff need to contact a person # knowledgable about the submission) _Mailing_address # MANDATORY _Phone_number # MANDATORY # [e.g.: ()x # 01 608 254-4511 x205] _Email_address # MANDATORY (n/a is acceptable) _FAX_number # Optional: same format as a phone # number # Primary contact person @ @ @ @ ; @ ; ; @ ; @ @ @ # Secondary contact person @ @ @ @ ; @ ; ; @ ; @ @ @ stop_ ######################################################################## # Example: # # # # loop_ # # _Family_name # # _Given_name # # _Middle_initials # # _Family_title # # _Department/Institution # # _Mailing_address # # _Phone_number # # _Email_address # # _FAX_number # # # # Doe John F. . # # # # ; Dept. of Biochemistry # # Univ. of Wisconsin # # ; # # # # ; 420 Henry Mall # # Madison WI USA 53706 # # ; # # # # '01 (555) 123-3456' # # jdoe@algf.rdw.edu # # '01 (555) 321-6543' # # # # West Gary L. . # # . # # . # # . # # . # # . # # . # # # # stop_ # # # ######################################################################## save_ ################################# # 3. Citation for this entry # ################################# # The experimental data and results in this deposition are assumed to # have originated from the single citation provided below. When # depositing data that span several citations, authors are requested # to break the results into separate deposition forms corresponding to # the individual publications. This can be accomplished easily by # completing one form and then using block copy commands found in most # word processors to copy the information that is common to all of the # deposition forms required. Values given the data tag # '_Related_BMRB_accession_number' (see Section 1) provide links that # identify data spanning multiple publications as forming a set. # If the data deposition is not related to a formal publication, use # this section to indicate all of the individuals responsible for the # work and enter 'BMRB' as the value for the tag '_Citation_BMRB_publ'. save_entry_citation # MANDATORY SAVE FRAME (use # data tags that apply) _Saveframe_category entry_citation _Citation_full # Generated by BMRB from the information @ # provided below. _Citation_title # MANDATORY ; @ ; _Citation_status # MANDATORY @ # Examples: [e.g.: published; # 'in press'; 'in preparation'] _Citation_type # Examples: [e.g.: journal; @ # book; thesis; abstract; # 'BMRB only'] _CAS_abstract_code # Supplied by BMRB @ _MEDLINE_UI_code # Supplied by BMRB @ loop_ # MANDATORY LOOP # Iterate once for each author _Author_ordinal # Integer value indicating # the order of the author's name # in the citation. _Author_family_name # MANDATORY (a name, even if it # is a single character, must be # entered for this data tag) _Author_given_name # Please provide the full given # name (excluding the family # name). First initials are acceptable # only if that is the form of your name # that you use for publications. _Author_middle_initials # Provide initials only for # names not previously entered. A full # middle name can be entered, if that is # the form of your name that you use for # publications. _Author_family_title # [e.g.: Sr.; Jr.; III; others] # # Author Family Given Initials Title # Ordinal Name Name # # ( 1 Doe John L.G. Sr. Example ) #----------------------------------------------------------------- # @ @ @ @ @ stop_ # Provide data values for the data tags that are appropriate for the # type of citation that is being described. _Journal_abbreviation # Please use Chemical Abstracts @ # Services journal abbreviations # whenever possible (ref 8). _Journal_name_full # Optional: Use only when an @ # official abbreviation is not # available. _Journal_volume @ # volume number _Journal_issue @ # issue number _Journal_ASTM @ # Supplied by BMRB _Journal_ISSN @ # Supplied by BMRB _Journal_CSD @ # Supplied by BMRB # For a book citation, please provide the applicable data. _Book_title @ _Book_chapter_title @ _Book_volume @ _Book_series @ _Book_publisher @ _Book_publisher_city @ _Book_ISBN @ # Supplied by BMRB # For an abstract citation, please provide the applicable data. _Conference_title @ _Conference_site @ _Conference_state_province @ _Conference_country @ _Conference_start_date @ _Conference_end_date @ _Conference_abstract_number @ # For a thesis, please provide the following information _Thesis_institution @ _Thesis_institution_city @ _Thesis_institution_country @ # For each class of publication, provide the page numbers and year below. _Page_first @ _Page_last @ _Year @ _Details # Optional: Text comment about the ; # publication. @ ; loop_ _Keyword # Keywords are VERY HELPFUL to # users who conduct data # searches. @ stop_ loop_ # Optional loop: # iterate once for each editor # (see the previous author loop # for descriptions of the # information requested) _Editor_ordinal _Editor_family_name _Editor_given_name _Editor_middle_initials _Editor_family_title # [e.g.: Sr.; Jr.; III; others] # # Editor Family Given Initials Title # Ordinal Name Name # # ( 1 Doe John L.G. Sr. Example ) #----------------------------------------------------------------- # @ @ @ @ @ stop_ save_ ###################################### # 4. Molecular system description # ###################################### # This section defines the macromolecules and small molecules that # form the system reported in this data block. The system may consist # of a single molecular species, e.g. ribonuclease, or it may contain # more than one kind of molecule, e.g. the tryptophan repressor - DNA # operator complex formed in the presence of tryptophan. Include all # molecular species that make up the macromolecular system even if # NMR data were not obtained for each species. Do not include unbound # solvent constituents such as buffers, salts, solvents, etc. as # these are described in Section 5.1 in which the contents of each # sample are listed. save_ # MANDATORY SAVE FRAME _Saveframe_category molecular_system _Mol_system_name # MANDATORY [e.g.: @ # 'holo trp repressor dimer- operator DNA complex' _Abbreviation_common # MANDATORY: Be very brief, under 20 @ # characters is recommended. _Enzyme_commission_number # Optional @ loop_ # Define the individual chemical units in the system. This # includes every instance of a biopolymer and/or ligand. _Mol_system_component_name # MANDATORY _Mol_label # MANDATORY @ @ stop_ #################################################################### # # Example: holo trp repressor dimer - trp operator DNA -tryptophan complex # # loop_ # _Mol_system_component_name # _Mol_label # # 'trp repressor subunit one' $trpR # 'trp repressor subunit two' $trpR # 'DNA strand one' $DNA_1 # 'DNA strand two' $DNA_2 # 'trp ligand one' $trp # 'trp ligand two' $trp # # stop_ # ##################################################################### _System_molecular_weight # in Daltons [e.g.: 17340] @ _System_physical_state # MANDATORY [e.g.: native; denatured; @ # 'molten globule'] _System_oligomer_state # For the system, indicate the @ # level of oligomerization observed or # known to exist [e.g.: monomer; dimer; # trimer; tetramer; 'double strand'; # etc.] _System_type # Select a keyword that best describes the complexity @ # of the system studied [e.g.: simple; complex; # multidomain; multimeric] simple indicates that the # system is made up of one type of biopolymer and does # not contain any ligands; a complex system contains # a biopolymer with bound ligands; a multimeric # system has more than one biopolymer, such # as a protein-DNA complex. _System_paramagnetic # MANDATORY [e.g.: yes, no] @ loop_ # Cond-MANDATORY: this loop is used to # define components of the system that # are magnetically equivalent, for # example both components of a # symmetrical dimer. _Magnetic_equivalence_ID # An identification code that defines # the set of equivalent components. _Magnetically_equivalent_system_component # Name for the system # component that is a # member of the set. @ @ stop_ ########################################################################## # Example: # # loop_ # _Magnetic_equivalence_ID # _Magnetically_equivalent_system_component # # 1 monomer-one # 2 monomer-two # # stop_ # ########################################################################## loop_ _Biological_function # Optional @ stop_ # The following loop is optional, but can be used to provide links to other # databases that contain information (structure, function, etc.) relevant to # the system described in this submission. This loop is not intended to be # used for links to sequence databases. loop_ _Database_name # Optional [e.g.: PDB; NDB] _Database_accession_code # Optional _Database_entry_mol_name # Optional: Name of the molecule used by # the database listed. _Database_entry_relation_type # BMRB inserted enumerated item # [e.g.: identical; homologous _Database_entry_details # Optional PDB @ @ @ ; @ ; CATH @ @ @ ; @ ; SCOP @ @ @ ; @ ; stop_ _Details # Optional: A text description for the ; # system. @ ; save_ ############################# # 4.1. Monomeric polymers # ############################# # Examples of the class of molecules described in this section would # include; ribonuclease, lysozyme, the A-chain of insulin, a single # strand of duplex DNA, a single RNA strand, an unbranched # carbohydrate polymer. save_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class # MANDATORY [e.g.: protein; DNA; RNA; @ # carbohydrate;] _Name_common # MANDATORY [e.g.: 'Staph. nuclease'] @ _Name_variant # Optional, use if appropriate @ # [e.g.: H124L] _Abbreviation_common # Optional: provide a common @ # acronym or mnemonic for the # molecule [e.g.: DHRF; ACP; RNase] _Name_CAS # Optional @ _CAS_registry_number # Optional @ _Enzyme_commission_number # Optional @ _Molecular_mass # Optional: in Daltons [e.g.: 12384] @ loop_ _Biological_function # Optional: only appropriate for systems @ # containing more than one kind of # polymer. The function of simple # systems is described above in # Section 4. stop_ _Details # Optional: text description for the ; # polymer @ ; loop_ _Synonym # Optional list of other names # used for a molecule # [e.g.: 'micrococcal nuclease']. @ stop_ ####################################### # 4.1.1. Polymer residue sequence # ####################################### # The sequence of a polymer (peptide, protein, nucleic acid, polymeric ligand) # is provided in the following loop. The tag '_Residue_label' is used to # define the type of residue at each position. If a code equal to one of # the standard one-letter or three-letter codes for amino acids and # nucleotides is used, it will be assumed that the chemical structure of # the residue corresponds to the appropriate amino acid or nucleotide # depending on the class of polymer defined above. Any non-standard # residues must be defined in section 4.2. below and must be given a unique # label. The value assigned to the tag '_Abbreviation_common' must be # identical to the value assigned to the '_Residue_label' tag in the following # loop. # In the event that a polymer is composed of a combination of residues # of differing type (e.g., a polymer of deoxyribose and ribose # nucleotides), the author must define the polymer of one and only one # class above. Majority rule should be used to define the polymer type # (i.e. protein, if the majority of residues are amino acids). Those # residues that are of the polymer type can be assigned standard # labels. Each residue of a minority polymer type must be # given a non-standard label value. One can simply indicate in the # non-standard constituent definition save frame (Section 4.2) that this is # a non-standard label for a residue of standard chemical structure rather # than entering the chemical structure. _Sequence_citation_label # Required if the sequence of the # molecule is not available from one # of the primary sequence data bases # listed below. # [e.g.: $citation_one] @ _Ambiguous_sequence_features # Cond-MANDATORY: Used to # characterize portions of the # sequence that are not known or may # be ambiguous. ; @ ; _Residue_count # Number of residues in the polymer @ _Mol_residue_sequence # Optional: similar to a FASTA # representation [e.g.: AGRTEDWQ] ; @ ; loop_ # MANDATORY LOOP _Residue_seq_code # MANDATORY # integer value that increases # sequentially beginning with 1. # Unambiguously defines the # order of the residues in the main # (non-branch)polymer chain. _Residue_author_seq_code # Optional: Author defined # sequence position code. The # value given this tag may refer # to a homologous sequence or define # a pro-peptide [e.g., 1; 3; 17a; # -1; or others]. _Insertion_code # Optional: Insertion codes are used # to align a mutant or variant # sequence with the native sequence # or sequence of a related polymer. _Residue_label # MANDATORY # Either use a one-letter or # three-letter code for a # standard biopolymer residue or # a common abbreviation described in # the saveframe for a non-standard # residue. # [e.g.: A; G; T; ala; ALA; dHyAla] _Segment_definition_code # Optional: A code inserted by the # author to define residues, for # example, belonging to unique # domains in a multidomain protein. # Residue Author Residue Insertion Residue Segment # Code Code Code Label Definition code #----------------------------------------------------------------------- @ @ @ @ @ stop_ loop_ _Database_name # MANDATORY [e.g.: SWISS-PROT; PDB; NDB; # PIR; GenBank] _Database_accession_code # MANDATORY _Database_entry_mol_name # Optional: Name of the molecule used by # the database listed. _Database_segment_ID # Optional: (i.e., domain definitions # or fold assignments) _Sequence_homology_type # BMRB supplied enumerated item # [e.g.: identical; homologous; # domain_homology] _Sequence_difference_details # Optional: useful if differences # exist between the molecule # studied and the molecule # refered to in a specified # sequence data base. _Sequence_alignment_details # Optional: results of a BLAST or FASTA # search GenBank @ @ @ @ ; @ ; ; @ ; SWISS-PROT @ @ @ @ ; @ ; ; @ ; PIR @ @ @ @ ; @ ; ; @ ; PDB @ @ @ @ ; @ ; ; @ ; stop_ save_ ############################ # 4.2. Polymer residues # ############################ # This section is required if a residue that is not one of the 20 common # amino acids or 8 common nucleotides (deoxyribose A, T, C, G and ribose A, # U, C, G, I) found in DNA and RNA is present in the system. save_ _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common # MANDATORY @ _Abbreviation_common # MANDATORY: provide a common @ # acronym or mnemonic for the # molecule [e.g.: PGA] _Name_IUPAC # Optional @ _Name_CAS # Optional: Name used for the @ # molecule by Chemical Abstracts # Service _CAS_registry_number # Optional @ _PDB_code ## If this deposition contains data @ ## intended to be included in the PDB, ## this abbreviation must be limited ## to three characters. [e.g.: PGA for ## pyroglutamate] _Standard_residue_derivative ## For PDB depositions, please ## indicate the standard biological ## residue that the non-standard ## residue is derived from if known. ## [e.g.: proline; glutamate, for ## hydroxy-proline and pyroglutamate, ## respectively] @ loop_ _Mol_label # Saveframe code for the molecule # where this non-standard residue is # located (from Section 4.1.) _Residue_seq_code # The sequence position(s) for the # residue. @ @ stop_ _Mol_empirical_formula # Chemical formula reported @ # using the 'Hill' System used by # CAS. In this system the number of # carbons and hydrogens are listed # first followed by other nuclei in # alphabetical order. # [e.g.: 'C2 H6 O1'] _Molecular_mass # in Daltons [e.g.: 784] @ _Mol_paramagnetic # MANDATORY [e.g.: yes; no] @ _Details # Optional text description ; @ ; _SMILES_representation # The SMILES representation for the @ # molecule can be given here. loop_ # Optional loop _Synonym @ stop_ # If this residue is part of a system whose atomic coordinates are # being reported, ASCII computer files may exist that describe the # structure of the residue. X-PLOR PSF structure files # are an example. The following three data tags can be used to # identify the names of files that accompany this data submission and # contain the structural information. These files are very useful in # accurately processing the submission of structural data. _Topology_file_name @ _Mol_structure_file_name @ _Mol_structure_file_format # [e.g.: ISIS; Chemdraw] @ _Stereochemistry_parameter_file_name @ # The next two loops provide a list of atoms in the molecule and # their connectivities. All atoms must be listed including hydrogens. loop_ _Atom_name # atom nomenclature; must be a # unique value for each atom in # the moiety defined in this # [e.g.: HB3; HG11] _Atom_type # [e.g.: H; C; N; O; P; S; Fe; Co] _Atom_chirality # MANDATORY for chiral and prochiral # centers [e.g.: R; S; pro-R; pro-S] _Atom_charge # Optional: Formal charge _Atom_oxidation_number # Optional: [e.g.: +2; +3; -1] _Atom_unpaired_electrons # Optional: [e.g.: 5; 3; 1] @ @ @ @ @ @ stop_ loop_ _Bond_order # MANDATORY [e.g.: single; double; # triple; aromatic; partial- # double] _Bond_atom_one_atom_name # MANDATORY, from the list given in # the loop_ above. _Bond_atom_two_atom_name # MANDATORY, from the list given in # the loop_ above. @ @ @ stop_ save_ ################### # 4.3. Ligands # ################### # The ligand section is used to define the chemical structures of # prosthetic groups, cofactors, metal ions, bound solvent, inhibitors, or # other small molecules that are part of the system studied. Ligands may or # may not be covalently linked to the biopolymer. If a covalent link exists, # the atoms involved in the bond and the type of bond must be described in # Section 4.4. save_ _Saveframe_category ligand _Mol_type non-polymer _Name_common # MANDATORY @ _Abbreviation_common # MANDATORY @ _Name_CAS # Optional @ _CAS_registry_number # Optional @ _Name_IUPAC # Optional @ _PDB_code ## Author recommended PDB code for a @ ## ligand that does not now exist in ## the PDB database. If this ## deposition contains data ## intended to be included in the PDB, ## this abbreviation must be limited ## to three characters. This is a ## designation suggested by the ## deposition author and may be ## altered by PDB [e.g.: PGA for ## pyroglutamate] _Mol_empirical_formula # Chemical formula reported @ # using the 'Hill' System used by # CAS. In this system the number of # carbons and hydrogens are listed # first followed by other nuclei in # alphabetical order. # [e.g.: 'C2 H6 O1'] _Molecular_mass # Optional @ _Mol_charge # Optional: Formal charge on the @ # molecule, if any. [e.g.: +1; +2; -1] _Mol_paramagnetic # MANDATORY [e.g.: yes; no] @ _Mol_aromatic # MANDATORY [e.g.: yes; no] @ loop_ _Biological_function # Optional @ stop_ _Details # Optional text description ; @ ; _SMILES_representation # The SMILES representation for the @ # molecule can be given here. loop_ # Optional loop _Synonym @ stop_ # If this molecule is part of a system whose atomic coordinates are # being reported, ASCII computer files may exist that describe the # structure of the molecule or residue. X-PLOR PSF structure files # are an example. The following three data tags can be used to # identify the names of files that accompany this data submission and # contain the structural information. These files are very useful in # accurately processing the submission of structural data. _Topology_file_name @ _Mol_structure_file_name @ _Mol_structure_file_format # [e.g.: ISIS; Chemdraw] @ _Stereochemistry_parameter_file_name @ # The next two loops provide a list of atoms in the molecule and # their connectivities. All atoms must be listed including hydrogens. # Do not use these loops, if the ligand is a small polymer and will be # described below by providing the sequence of the polymer loop_ _Atom_name # atom nomenclature; must be a # unique value for each atom in # the moiety defined in this # [e.g.: HB3; HG11] _Atom_type # [e.g.: H; C; N; O; P; S; Fe; Co] _Atom_chirality # MANDATORY for chiral and prochiral # centers [e.g.: R; S; pro-R; pro-S] _Atom_charge # Optional: Formal charge _Atom_oxidation_number # Optional: [e.g.: +2; +3; -1] _Atom_unpaired_electrons # Optional: [e.g.: 5; 3; 1] @ @ @ @ @ @ stop_ loop_ _Bond_order # MANDATORY [e.g.: single; double; # triple; aromatic; partial- # double] _Bond_atom_one_atom_name # MANDATORY, from the list given in # the loop_ above _Bond_atom_two_atom_name # MANDATORY, from the list given in # the loop_ above @ @ @ stop_ loop_ _Database_name # Optional [e.g.: PDB; NDB; CCDC] _Database_accession_code # Optional _Database_entry_mol_name # Optional: Name of the molecule used by # the database listed. _Database_entry_details # Optional @ @ @ @ stop_ save_ ############################################### # 4.4. Molecular bond linkage definitions # ############################################### # The following two loops are used if needed to fully characterize # the chemical structure of a monomeric biopolymer, complex or multimeric # molecule (e.g., bonds linking non-standard residues in a biopolymer, the # copper ligand bonds in plastocyanin or the iron-cysteine bonds in # ferredoxin, links in branched polymers such as glycoproteins). The first # loop defines the bond that is made in terms of the two atoms and the bond # between them. The second loop specifies which atoms normally present have # been deleted. Each loop can be iterated as many times as needed. save_crosslink_bond_definitions # Optional saveframe _Saveframe_category crosslink_bonds loop_ _Bond_order # MANDATORY [e.g.: single; double; # triple; aromatic; partial- # double] _Bond_type # Optional [e.g.: peptide; # disulfide; amide] _Atom_one_mol_system_component_name # MANDATORY # [e.g.: A1; B2; peptide; Cu] _Atom_one_residue_seq_code # Optional, required if needed to # locate the atom _Atom_one_residue_label # Optional _Atom_one_atom_name # MANDATORY _Atom_two_mol_system_component_name # MANDATORY _Atom_two_residue_seq_code # Optional _Atom_two_residue_label # Optional _Atom_two_atom_name # MANDATORY _Details # Optional @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Deleted_atom_mol_system_component_name # MANDATORY _Deleted_atom_residue_seq_code # Cond-MANDATORY _Deleted_atom_residue_label # Cond-MANDATORY _Deleted_atom_name # MANDATORY # # Molecule Residue Residue Atom # Component Number Label Name # Name #---------------------------------------- # @ @ @ @ stop_ save_ ######################################################### # 4.5. Biologically functional molecule descriptions # ######################################################### save_ _Saveframe_category biol_func_molecular_system _Name_common @ _Abbreviation_common # MANDATORY @ _Enzyme_commission_number @ _Details ; @ ; loop_ _Mol_system_component_name # Use this loop to list the # components of the system that # are part of the biologically # functional macromolecule described # in this saveframe. @ stop_ loop_ _Biological_function # Optional @ stop_ loop_ _Database_name # Optional [e.g.: PDB; NDB] _Database_accession_code # Optional _Database_entry_mol_name # Optional: Name given the molecule by # the listed database. _Database_entry_details # Optional @ @ @ @ stop_ save_ ########################## # 4.6. Natural source # ########################## # This save frame is used to describe the organism and the portion of # the organism that is the natural source for a molecule. A save # frame of this type is MANDATORY for each polymer that is defined as # a member of the system studied, if the molecule has a known natural # source. Many times a mutant of a natural biomolecule is # investigated. In these cases, please provide information describing # the source of the wild type molecule. For molecules not # obtained from a natural source, use Section 4.7. and indicate a # vendor, if purchased, and/or method of production. For chimeric # molecules, please complete a saveframe like the one below for each # member of the chimera that has a different natural source. save_natural_source _Saveframe_category natural_source loop_ _Mol_label # MANDATORY [e.g.: $hemoglobin; # $plastocyanin] # Framecodes: # $ # $ # $ _Organism_name_common # MANDATORY _Organism_acronym # Optional _ICTVdb_decimal_code # International Committee on Taxonomy # of Viruses decimal code # [e.g.: 61.0.6.5.001] _NCBI_taxonomy_ID # [e.g.: 11676 _Superkingdom # [e.g.: eucaryote; eubacteria; # archaea; virus; viroids (plasmids); # other] _Kingdom # [e.g.: Animalia; Plantae; Protista; # Fungi; Monera ] _Genus # MANDATORY [e.g.: Escherichia] _Species # MANDATORY [e.g.: coli] _Strain # Applies to both cellular organisms # and viruses [e.g.: K12] _Variant # Applies to both cellular organisms # and others (viruses, plasmids, etc.) _Subvariant # Applies to both cellular organisms # and others (viruses, plasmids, etc.) _Organ # [e.g.: heart; brain; lung; etc.] _Tissue # [e.g.: 'striated muscle'; etc.] _Cell_line # [e.g.: 'HELA cells'] _Cell_type # [e.g.: T-lymphocytes] _ATCC_number # American Type Culture Collection _Organelle # [e.g.: mitochondria; chloroplast; # nucleus; 'golgi apparatus'; # 'endoplasmic reticulum'; # others] _Fraction # [e.g.: cytoplasm; periplasm; others] _Secretion # [e.g.: venom _Plasmid # [e.g.: ColE1] _Gene_mnemonic # [e.g.: lac; trpR] _Details # text comment @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ save_ ############################################################################# # Kingdom Definitions # # # # Animalia: Multi-cellular motile organisms that feed heterotrophically # # Plantae: Multi-cellular organisms which feed by photosynthesis # # Protista: Protozoa and single-celled algae # # Fungi: Fungi # # Monera: Procaryotes and cyanobacteria # # # # Reference: URL: http://fac1.vet.ed.ac.uk/tol/kingdoms.htm # # Synopsis and Classification of Living Organisms (Volume 2), edited by # # S.P. Parker Published by McGraw-Hill Book Company in 1982. # # ISBN 0-07-079031-0 (set), # # # #---------------------------------------------------------------------------# # Virus Taxonomy # # # # Virus taxonomy is described at the following WWW site: # # # # http://www.ncbi.nlm.nih.gov/ICTV/ # # # ############################################################################# ################################ # 4.7. Experimental source # ################################ # Please complete this section for all molecules. This save frame can be # used to describe the source of purchased material or to indicate # compounds that were chemically synthesized or obtained by biosynthetic # means. Create a save frame, if appropriate, for each molecule defined as # a member of the system studied. # For molecules produced through recombinant technology, the host- # vector system used to generated the molecule is given in the # following section. The natural source for a molecule must be # supplied in Section 4.6. Please repeat this save frame for each # molecule in the system produced by recombinant technology or for # each host-vector system used to generate a molecule. Only those # data tags that are applicable need to be completed. save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label # MANDATORY [e.g.: $hemoglobin; # $plastocyanin] # Framecodes: # $ # $; # $ _Production_method # [e.g.: 'chemical synthesis'; # 'cell free synthesis'; # 'enzymatic semi-synthesis'; # 'recombinant technology'; # 'purified from the natural source'] _Host_organism_name_common # [e.g.: 'E. coli'; yeast; # 'CHO cells'] _Genus # Host genus _Species # Host species _Strain # Host strain _Variant # Host variant _Organ # [e.g.: ovary] _Tissue # Tissue used as production source _Cell_line # Host cell line _Cell_type # [e.g.: T-lymphocytes] _ATCC_number # Host ATCC number _Vector_type # [e.g.: plasmid; cosmid; virus] _Vector_name # [e.g.: pBR322] _Vendor_name # [e.g.: Sigma; Worthington] _Gene_source _Details @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ save_ ######################################### # 5. Sample contents and methodology # ######################################### ############################## # 5.1. Sample description # ############################## # Create a save frame, as outlined below, for at least one representative # sample. save_ # MANDATORY # At least one sample must be # described to provide a # complete definition of the # conditions used in collecting # the data reported in the # deposition form. _Saveframe_category sample _Sample_type # [e.g.: solution; solid; emulsion; gel; @ # Bi-cell] _Details # Optional text description ; @ ; loop_ _Mol_label # MANDATORY [e.g.: $hemoglobin; $FAD; # $plastocyanin] # Framecodes: # $ # $ # $ # $ # If the molecule is a buffer, # salt,or other constituent that # has not been assigned a # framecode then provide a # specific name. # [e.g.: sodium phosphate'; # 'sodium chloride'; # 'potassium chloride'; # 'TRIS buffer'; CHAPS; DSS; # TSP; etc.] _Concentration_value # PREFERRED _Concentration_value_units # MANDATORY _Concentration_min_value # Optional _Concentration_max_value # Optional _Isotopic_labeling # If the molecule studied has been # isotopically labeled, provide a # description of the labeling using # the methods recommended by the # current IUPAC/IUBMB/IUPAB # Interunion Task Group # Molecule Conc. Conc. Conc. Conc. Isotopic # Label Value Units Min-value Max-value Labeling # (Min. and Max. values) # (are NOT preferred) # ------------------------------------------------------------------- # # (Example:) # $Snase 1.5 mM . . [U-15N] # @ @ @ @ @ @ ########################################################################## # Examples for describing isotopically labeled molecules. # # # # 1. Uniform (random) labeling with 15N: [U-15N] # # 2. Uniform (random labeling with 13C, 15N (labeling levels known: # # '[U-95% 13C; U-90% 15N]' # # 3. Residue-selective labeling: '[98% 15N]-His' # # 4. Site specific labeling: '[95% 13CA]-Trp28' # # 5. Natural abundance isotopic labeling of otherwise uniformly labeled # # biopolymers are designated by NA for natural abundance: # # '[U-95% 2H; NA-I,L,V]' # # # ########################################################################## stop_ save_ ################################### # 5.2. Purity of the molecules # ################################### # Please indicate the purity of each molecule relevant to the study # within this save frame and the method used to quantify the purity. save_sample_mol_purity # Optional save frame _Saveframe_category sample_mol_purity _Details ; @ ; _Sample_label @ loop_ _Mol_label # MANDATORY [e.g.: $hemoglobin; $FAD; # $plastocyanin] _Mol_purity_value # [e.g.: 95] _Mol_purity_value_units # [e.g.: %] _Mol_purity_measurement_method # [e.g.: 'SDS gel electrophoresis'; # 'mass spectrometry'; etc.] @ @ @ @ stop_ save_ ################################ # 6. Computer software used # ################################ # Providing the information described in section 6 is optional. # List each computer program used to acquire, process, or analyze the # data reported in this submission. The character string assigned to # is used in later sections to define specific # software products used to manipulate individual sets of data. save_ # Optional save frame # Use only the data tags that # are appropriate. _Saveframe_category software _Name # MANDATORY: may include data # processing as well as data # caluculation and structure # calculation software [e.g.: FELIX; # NMR-PIPE; X-PLOR; DGII; CONGEN; # DIANA; DSPACE; DGEOM] @ _Version @ loop_ _Vendor # MANDATORY [e.g.: Biosym; Bruker; # MSI; Tripos; Varian] _Address # Optional text field _Electronic_address # URL or other site where # software can be obtained or is # described. @ ; @ ; @ stop_ loop_ _Task # give a very concise description # of the task that the software # performed (many software packages # perform a variety of tasks, a brief # list of the most important tasks # can be given here) [e.g.: 'raw # spectral data (FID) # transformations'; 'peak picking'; # 'structure calculation'; energy # minimization] @ stop_ loop_ _Platform_vendor # Optional [e.g.: DEC; HP; IBM; SGI; # SUN] _Platform_model # Optional [e.g.: RS6000; Spark-10; # Indy] _Operating_system # Optional _Operating_system_version # Optional _Hardware_code # Optional (i.e., CPU name) @ @ @ @ @ stop_ _Citation_label # [e.g.: $citation_4] @ save_ ############################# # 7. Experimental detail # ############################# # Create a saveframe like this one for each relevant experiment (usually # NMR experiments) that was conducted in this study. ######################################## # 7.1. NMR Spectrometer definitions # ######################################## save_ # Optional save frame, use only # the appropriate data tags. # This save frame must be # repeated for each # spectrometer. _Saveframe_category NMR_spectrometer _Manufacturer # [e.g.: Bruker; JEOL; Varian] @ _Model # [e.g.: DMX500; Unity-Plus] @ _Field_strength # 1H frequency in MHz[e.g.: 500; @ # 750] _Software_version_number @ _Details # Describe any modifications # made to the instrument or # other details of interest. ; @ ; save_ #################################### # 7.2. NMR applied experiments # #################################### # This save frame should be replicated for each NMR experiment that # was used to derive the experimental results described below. # The following information, in particular an ASCII file containing # the pulse sequence used in the experiment, will allow BMRB to # provide users with up-to-date versions of NMR experiments that have # worked on a particular spectrometer. save_ # Optional save frame _Saveframe_category NMR_applied_experiment _Experiment_name # [e.g.: COSY; NOESY; HN(CA)CO; # ROESY; 'HCCH E.COSY'] @ _Sample_label # [e.g.: $sample_1] @ _BMRB_pulse_sequence_accession_number # The ID value is taken from @ # the BMRB Pulse sequence # library. _Pulse_sequence_file_name # If file name values are @ # provided for a 'file_name # tag, the file must be # attached to the submission. _Pulse_sequence_parameter_file_name # Attach file @ _Pulse_sequence_schematic_file_name # Attach file @ _Pulse_sequence_schematic_file_format # Examples: [e.g.: postscript; @ # TIFF; GIF] loop_ _Citation_label # Framecode for citation for the @ # expt. [e.g.: $citation_3] stop_ _Details # Text description ; @ ; ################################################# # 7.2.1. NMR spectral acquisition parameters # ################################################# loop_ _Acquisition_dimension_ID # A value that defines the # dimension of the experiment # that the following values # pertain. [e.g.: t1; D1] _Detected_atom_type # MANDATORY [e.g.: H; C; N; O; S; P] _Spectrometer_carrier_frequency # [e.g.: 117.9ppm; 500.132405MHz] _Acquisition_time # [e.g.: 23.3ms] _Mixing_time # [e.g.: 100ms] _Spectral_width # [e.g.: 1422Hz] _Spectral_folding # [e.g.: yes; no] _Data_point_number # [e.g.: 64] _Data_point_type # [e.g.: real; complex] _Data_point_spacing # [e.g.: linear; non-linear] @ @ @ @ @ @ @ @ @ @ stop_ ################################################ # 7.2.2. NMR spectral processing parameters # ################################################ loop_ _Processing_dimension_ID # A value that defines the # dimension of the experiment # that the following values # pertain. [e.g.: f1; D1] _Exponential_factor # [e.g.: 5; -3] _Gaussian_factor # [e.g.: 0.043] _Processed_real_points # [e.g.: 256] @ @ @ @ stop_ save_ ########################### # 8. Sample conditions # ########################### # Completion of section 8 is MANDATORY. # This section is used to explicitly define the conditions under # which specific NMR data (chemical shift values, coupling constants, # conformers, etc.) reported in the sections below were determined. # Where sets of data were determined under different conditions, a # specific save frame of this type must be created to report each set # of conditions used. These save frames will be referenced in the # sections where the actual data are listed. For example, if one set # of chemical shifts was determined at pH 7 and a second set # determined at pH 4, then two save frames must be created, one # defining pH 7 and one defining pH 4 as the conditions used. Later # two save frames, one for each set of chemical shifts would be # created. Within those chemical shift save frames, the save frame # containing appropriate experimental conditions would be referenced. # Sample deposition forms available from the BMRB WWW site # demonstrate how this save frame is used. save_ # MANDATORY SAVE FRAME # [e.g.: save_conditions_1] _Saveframe_category sample_conditions _Details # Optional text comment ; @ ; loop_ _Variable_type # MANDATORY [e.g.: pH; temperature; # pressure;] _Variable_value # [e.g.: 5.6; 35] _Variable_value_error # [e.g.: 0.01; 1; 0.2] _Variable_value_units # Please use SI units # # Variable Value Error Units # ---------------------------------------------- # pH @ @ @ temperature @ @ @ pressure @ @ @ 'ionic strength' @ @ @ viscosity @ @ @ 'dielectric constant' @ @ @ stop_ save_ ######################## # 9. NMR parameters # ######################## #################################### # 9.1. Assigned chemical shifts # #################################### ######################################## # 9.1.1. Chemical shift referencing # ######################################## save_ # MANDATORY SAVE FRAME when # chemical shift data are # reported below. _Saveframe_category chemical_shift_reference _Details # Comment concerning referencing ; @ ; loop_ _Mol_common_name # [e.g.: TSP; DSS; Dioxane] # Use all data tags that apply. # Please comment out or delete # data tags that are not used. _Atom_type # [e.g.: H; C; N; P; S; Cd] _Atom_isotope_number # [e.g.: 1; 2; 13; 31] _Atom_group # [e.g.: methyl; methylene] _Chem_shift_units # [e.g.: ppm; Hz] _Chem_shift_value # in ppm [e.g.: 0; 4.78; 21.6] _Reference_method # [e.g.: internal; external] _Reference_type # [e.g.: direct; indirect] _External_reference_sample_geometry # [e.g.: cylindrical; # spherical] _External_reference_location # [e.g.: 'in the sample'; # 'external to the sample'] _External_reference_axis # Orientation with respect to # Bo. [e.g.: parallel; # perpendicular] _Indirect_shift_ratio _Indirect_shift_ratio_citation_label # [e.g.: $citation_one] _Reference_correction_type # [e.g.: temperature, pH, # etc.] _Correction_value _Correction_value_citation_label # [e.g.: $citation_three] @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 9.1.2. Assigned chemical shift lists # ########################################### # Chemical shift data and supporting experimental details are # organized in this save frame. Authors are asked to define the # ambiguity of each assignment using the codes defined below. # For a system that contains multiple components, a save frame like this one # should be created for each unique molecular entity in the complex (i.e., one # for the protein in flavodoxin and one for the flavin). ################################################################### # Chemical Shift Ambiguity Code Definitions # # # # Index Code Definition # # # # 1 Unique # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 3 Aromatic atoms on opposite sides of the ring # # (e.g. Tyr HE1 and HE2 protons) # # 4 Intraresidue ambiguities (e.g. Lys HG and # # HD protons) # # 5 Interresidue ambiguities (Lys 12 vs. Lys 27) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_ _Saveframe_category assigned_chemical_shifts _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1] # (see Section 8, above) _Chem_shift_reference_set_label # MANDATORY @ _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known, the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ # These tags are used to define _Nucleus # uniform chemical shift error values _Chemical_shift_error # that apply to all nuclei of the type # specified in the chemical shift table. 1H @ 2H @ 3H @ # These tags will be removed from the 13C @ 15N @ 19F @ # final entry by BMRB and the values 31P @ # inserted into the chemical shift # table. stop_ loop_ _Atom_shift_assign_ID # MANDATORY Unique ID used in the # following save frame to # identify atoms involved in # ambiguous chemical shift # assignments. _Residue_seq_code # Optional, MANDATORY for biopolymers # but not for ligands [e.g.: 1; 2; 3; 4] # Residue number in the polymer # sequence. Must correlate with # the values assigned in # Section 4.1.1. _Residue_label # Optional, MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_type # MANDATORY [e.g.: H; C; N; O; S; P] _Chem_shift_value # MANDATORY in ppm _Chem_shift_value_error # MANDATORY _Chem_shift_ambiguity_code # MANDATORY # #Atom-shift Residue Residue Atom Atom Shift/ Error/ Ambiguity #Assign_ID Seq_code Label Name Type ppm ppm Code #------------------------------------------------------------------- # 1 1 ALA HB H 1.35 0.01 1 (Example) # # (An ASCII table of chemical shifts following this format can be # (taken from another source and pasted into the form at this point # (using a text editor.) @ @ @ @ @ @ @ @ stop_ # The following loop is used to define sets of Atom-shift assignment IDs that # represent related ambiguous assignments taken from the above list of # assigned chemical shifts. Each element in the set should be separated by a # comma as shown in the example below and is the assignment ID for a chemical # shift assignment that has been given an ambiguity code of 4 or 5. Each set # indicates that the observed chemical shifts are related to the defined # atoms, but have not been assigned uniquely to a specific atom in the set. loop_ _Atom_shift_assign_ID_ambiguity # # Sets of Atom-shift Assignment Ambiguities # # ------------------------------------------ # Example: 5,20,47 # @ stop_ save_ ############################# # 9.2. Coupling constants # ############################# save_ _Saveframe_category coupling_constants _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Spectrometer_frequency_1H # Optional @ _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Coupling_constant_code # MANDATORY [e.g.: 3JHNHA] _Atom_one_residue_seq_code # Cond-MANDATORY (i.e., mandatory if the # system component is a polymer # [e.g.: 1; 2; 3; 4] _Atom_one_residue_label # Cond-MANDATORY _Atom_one_name # MANDATORY [e.g.: HB3; HG11] _Atom_two_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_two_residue_label # Cond-MANDATORY _Atom_two_name # MANDATORY [e.g.: HB3; HG11] _Coupling_constant_value # Cond-MANDATORY _Coupling_constant_min_value # Cond-MANDATORY _Coupling_constant_max_value # Cond-MANDATORY _Coupling_constant_value_error # MANDATORY ('?' is a valid value) @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ######################### # 9.3. T1 relaxation # ######################### save_ _Saveframe_category T1_relaxation _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Spectrometer_frequency_1H # MANDATORY @ _T1_coherence_type # MANDATORY (text description @ # that describes the nuclei # involved in the measured # coherence) Examples: [e.g.: Nz; Cz; # NzHz; etc.] _T1_value_units @ # MANDATORY [e.g.: s; ms; s-1] defines # the form of the data reported (time or # rate) _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known, the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: N] _T1_value # MANDATORY _T1_value_error # MANDATORY @ @ @ @ @ stop_ save_ ############################ # 9.4. T1rho relaxation # ############################ save_ _Saveframe_category T1rho_relaxation _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Spectrometer_frequency_1H # MANDATORY @ _T1rho_coherence_type # MANDATORY (text description @ # that defines the nuclei # involved in the measured # coherence) _T1rho_value_units @ # MANDATORY - defines the form of the # data reported (time or rate) _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known, the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: N] _T1rho_value # MANDATORY _T1rho_value_error # MANDATORY @ @ @ @ @ stop_ save_ ######################### # 9.5. T2 relaxation # ######################### save_ _Saveframe_category T2_relaxation _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Spectrometer_frequency_1H # MANDATORY @ _T2_coherence_type # MANDATORY (text description @ # that defines the nuclei # involved in the measured # coherence) _T2_value_units @ # MANDATORY # _Rex_units @ # used when exchange values are # reported _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: N] _T2_value # MANDATORY _T2_value_error # MANDATORY _Rex_value # Optional _Rex_error # Optional @ @ @ @ @ stop_ save_ ############################# # 9.6. Heteronuclear NOE # ############################# # This section of the form is designed to capture intraresidue # heteronuclear NOE data. save_ _Saveframe_category heteronuclear_NOE _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Spectrometer_frequency_1H # MANDATORY @ _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Atom_one_atom_name # MANDATORY [e.g.: N] @ _Atom_two_atom_name # MANDATORY [e.g.: H] @ _Heteronuclear_NOE_value_type # MANDATORY [e.g.: 'peak height'; @ # 'peak integral'; 'contour count'; # 'relative intensities'] _NOE_reference_value # MANDATORY: value used to calibrate @ # other NOE measurements _NOE_reference_description # MANDATORY @ _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Heteronuclear_NOE_value # MANDATORY _Heteronuclear_NOE_value_error # Optional @ @ @ @ stop_ save_ ########################### # 9.7. Homonuclear NOE # ########################### save_ _Saveframe_category homonuclear_NOE _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Homonuclear_NOE_value_type # MANDATORY [e.g. 'build up rate'; @ # 'peak height'; 'peak intensity'; # 'contour count'] _NOE_reference_value # MANDATORY: value used to calibrate @ # other NOE measurements _NOE_reference_description # MANDATORY: describe the reference @ # [e.g.: 'Gly 24 HA2-HA3 NOE peak'] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Atom_one_mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Atom_one_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_one_residue_label # Cond-MANDATORY _Atom_one_atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_two_mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Atom_two_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_two_residue_label # Cond-MANDATORY _Atom_two_atom_name # MANDATORY _Homonuclear_NOE_value # MANDATORY _Homonuclear_NOE_value_error # Optional @ @ @ @ @ @ @ @ @ @ stop_ save_ ############################## # 9.8. Spectral peak list # ############################## save_ _Saveframe_category spectral_peak_list _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ _Experiment_label # Framecodes for @ # experiments listed in Section 7. _Number_of_spectral_dimensions # The number of processed spectral # dimensions in the spectrum @ loop_ _Expt_dimension_ID # Integer value for processed spectral # dimension _Atom_type # [e.g.: 1H; 2H; 13C; 15N] _Spectral_region # region of the spectrum observed for # the atom type specified [e.g.: H; # CA/CB; C; N] @ @ @ stop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Peak_list_number # An integer defining the peak # number _Dim_1_chem_shift # Measured chemical shift _Mol_system_component_name _Residue_seq_code _Residue_label _Atom_name _Dim_2_chem_shift _Mol_system_component_name _Residue_seq_code _Residue_label _Atom_name _Dim_3_chem_shift _Mol_system_component_name _Residue_seq_code _Residue_label _Atom_name _Dim_4_chemical_shift _Mol_system_component_name _Residue_seq_code _Residue_label _Atom_name _Intensity_volume # Report either the volume or height _Intensity_height _Intensity_error @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ ############################################################## # # # Additional tags that could be included in the above loop: # # # # _Dim_1_line_width # # _Dim_2_line_width # # _Dim_3_line_width # # _Dim_4_line_width # # # # _Dim_1_Phase # # _Dim_2_Phase # # _Dim_3_Phase # # _Dim_4_Phase # # # # _Dim_1_Decay_rate # # _Dim_2_Decay_rate # # _Dim_3_Decay_rate # # _Dim_4_Decay_rate # # # ############################################################## save_ ############################# # 10. Kinetic parameters # ############################# ############################# # 10.1. Order parameters # ############################# # Lipari and Szabo (ref. 14, 15) first described the interpretation of # NMR relaxation experiments using a generalized order parameter and # an effective correlation time. Since that publication, several # extensions to this method or related formalisms have been devised. # Each of these involves the calculation of additional parameters and # the data have been reported in a variety of forms. In this section, # data tags are provided for reporting data as described by Lipari and # Szabo. Included in the loop, but commented out, are several # additional data tags that represent a number of additional # parameters related to NMR relaxation data and order parameters that # have been published. Please make use of these data tags in the # appropriate loop, if needed, to properly represent the data being # reported. # Given the variety of methods used to derive order parameters, # please provide the citation to the formalism you have used. save_ _Saveframe_category S2_parameters _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Tau_e_value_units @ # _Tau_s_value_units @ _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: N] _Model_fit _S2_value # MANDATORY _S2_value_fit_error # MANDATORY _Tau_e_value _Tau_e_value_fit_error @ @ @ @ @ @ @ @ ###################################################### # Additional Potentially Useful Data Tags # # # # _S2f_value # # _S2f_value_fit_error # # _S2s_value # # _S2s_value_fit_error # # _Tau_s_value # # _Tau_s_value_fit_error # # _S2H_value # # _S2H_value_fit_error # # _S2N_value # # _S2N_value_fit_error # # # ###################################################### stop_ save_ ############################# # 10.2. H-exchange rates # ############################# save_ _Saveframe_category H_exchange_rate _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _H_exchange_rate_units # MANDATORY @ # Placing this item here outside # of the data loop given below # forces the use of one unit in # the following loop where the # data are listed. If it is # appropriate to report data # values using more than one # type of unit, place this data # tag in the loop below and # define the units for each H- # exchange rate listed. _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] # [e.g.: A1; B2; H1; peptide; Cu] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY [e.g.: ALA; ASN] _Atom_name # MANDATORY [e.g.: H; HD21] _H_exchange_rate_value # Optional _H_exchange_rate_min_value # Optional: For very slowly # exchanging protons, the value may # represent a minimum value. _H_exchange_rate_max_value # Optional: value might relate to the # dead time of the experiment. _H_exchange_rate_value_error # MANDATORY @ @ @ @ @ @ @ stop_ save_ ########################################## # 10.3. H-exchange protection factors # ########################################## # Create a save frame block for each set of experimentally reported # protection factors determined under a defined set of conditions and # using a unique set of standard H-exchange rates. save_ _Saveframe_category H_exchange_protection_factors _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Standard_values_source_citation_label # MANDATORY: defines the @ # source for the standard # H-exchange rate values # used to calculate the # protection factors. _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] # [e.g.: A1; B2; H1; peptide; Cu] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY [e.g.: ALA; ASN] _Atom_name # MANDATORY [e.g.: H; HD21] _H_exchange_protection_factor_value # MANDATORY _H_exchange_protection_factor_value_error # Optional @ @ @ @ @ stop_ save_ ############################################################# # 10.4. Combined H-exchange rates and protection factors # ############################################################# # Create a save frame block for each set of experimentally reported # protection factors determined under a defined set of conditions and # using a unique set of standard H-exchange rates. save_ _Saveframe_category H_exchange_and_protection_factors _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Standard_values_source_citation_label # MANDATORY: defines the @ # source for the standard # H-exchange rate values # used to calculate the # protection factors. _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: H; HD21] _H_exchange_rate_value # Optional _H_exchange_rate_min_value # Optional _H_exchange_rate_max_value # Optional _H_exchange_rate_value_error # Optional _H_exchange_protection_factor_value # MANDATORY _H_exchange_protection_factor_value_error # Optional @ @ @ @ @ @ @ @ @ stop_ save_ ################################### # 11. Thermodynamic parameters # ################################### ####################### # 11.1. pKa values # ####################### save_ _Saveframe_category pKa_value_data_set _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Expt_observed_parameter # MANDATORY [e.g.: 'chemical shift'; @ # 'line width'] _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _pKa_list_number # Optional: an Id to be used in # the accompanying save frame # where specific parameter # values can be listed as a # function of pH. _Atom_observed_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_observed_residue_label # Optional (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_observed_atom_name # MANDATORY [e.g.: HB3; HG11] _pKa_hill_coeff_value _pKa_hill_coeff_value_fit_error _High_pH_parameter_fit_value _High_pH_parameter_fit_value_error _Low_pH_parameter_fit_value _Low_pH_parameter_fit_value_error _pKa_value _pKa_value_fit_error # The titrating hydrogen, if known, should be defined with this series # of identifiers. _Atom_titr_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_titr_residue_label # Cond-MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_titr_atom_name # MANDATORY [e.g.: HB3; HG11] @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 11.1.1. pH versus NMR parameter list # ########################################### # The paired pH values and observed NMR parameter values used to # fit a pKa value can be listed in this save frame. save_ _Saveframe_category pH_NMR_parameter_list _pKa_value_data_set_label # Save frame code for the @ # related set of pKa values. _Details # Optional descriptive comment ; # about the data. @ ; _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ # Optional Loop _pKa_list_number # ID value taken from the # pKa_value save frame. _pH_value _pH_value_error _Observed_NMR_parameter_value _Observed_NMR_parameter_value_error @ @ @ @ @ stop_ save_ ###################################### # 11.2. D/H-fractionation factors # ###################################### save_ _Saveframe_category D/H_fractionation_factor _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY [e.g.: ALA; ASN] _Atom_name # MANDATORY [e.g.: H; HD21] _H_fractionation_value _H_fractionation_value_error @ @ @ @ @ stop_ save_ ####################################### # 12. Secondary structure features # ####################################### # This section is used to describe secondary structure features # derived from a quantitative analysis of the data. ############################################################ # 12.1. Structure features derived from chemical shifts # ############################################################ save_ _Saveframe_category secondary_structure _Details # Optional descriptive comment ; # about the data. @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) loop_ # MANDATORY LOOP _Expt_applied_data_set_label # Listed here are the save # frame $framecodes from above # for the save frames # containing quantitative # results used in determining # the secondary structure # elements reported below. # (e.g., chemical shifts or # coupling constants) @ stop_ _Residue_struct_value_details # MANDATORY: Text describing the ; # method used to derive the @ # quantitative value given in ; # the following loop (e.g., # Chemical shift index # calculated according to # Wishart et al.) loop_ _Protocol_citation_label # Optional: Bibliographic @ # reference for method used to # calculate the values reported # for _Residue_struct_value. # [e.g.: $citation_one] stop_ _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code # MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_name # MANDATORY [e.g.: HB3; HG11] _Residue_struct_value # Optional _Residue_struct_element_type # See detailed instructions for # a list of allowed values # for this data tag. @ @ @ @ @ stop_ save_ ################################### # 12.2. Deduced hydrogen bonds # ################################### # This section of the form is designed for designating the proton and # heavy atom involved in a hydrogen bond that has been deduced from # H-exchange data, NOE/ROE data, secondary structure analysis or other # experimental evidence. save_ _Saveframe_category deduced_hydrogen_bonds _Details # MANDATORY descriptive comment # defining how the H-bonds have # been deduced. ; @ ; # Software applications used to generate the data in this saveframe. loop_ # Optional Loop _Software_label # Framecodes for save frames defined # in Section 6. @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Protocol_citation_label # Optional: Bibliographic @ # reference for the method used to # calculate the values reported. # [e.g.: $citation_one] stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Atom_one_mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Atom_one_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_one_residue_label # Cond-MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_one_atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_two_mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Atom_two_residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Atom_two_residue_label # Cond-MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_two_atom_name # MANDATORY @ @ @ @ @ @ @ @ stop_ save_ ######################################################## # 13. Atomic coordinates in three dimensional space # ######################################################## ################################################## # 13.1. Structure statistical characteristics # ################################################## save_ _Saveframe_category conformer_statistical_characteristics _Details ; @ ; _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; _Original_conformer_statistics_file_ID # Supplied by BMRB to provide a @ # link to the original data # deposited by the author _Conformer_family_label # MANDATORY: saveframe code @ # for the atomic coordinates for # the family of conformers _Representative_conformer_label # Cond-MANDATORY: required if @ # coordinates and statistics # are supplied for a # representative conformer _Conformer_calculated_total_number # MANDATORY: if due to the # methods used this number # cannot be provide, describe # the reasons as text provided # as a value to the 'detail' # data tag given above. @ _Conformer_submitted_total_number # MANDATORY: must match @ # the number of conformers # submitted. _Conformer_selection_criteria # MANDATORY: text @ # description of the # criteria used to select # the conformers # submitted. # The following two data tags are used to define the single conformer # from the family of conformers that is most representative of the # family of structures. This information is not needed if an energy # minimized average structure or another form of a representative # structure for the ensemble is provided in Section 15.4. _Rep_structure_conformer_number @ _Rep_structure_selection_criteria # Describe the criteria used # to selected the # representative conformer. ; @ ; loop_ _Constraint_list_label # Provide the saveframe codes for the # constraint lists used to compile # the following statistics. @ stop_ loop_ # MANDATORY loop _Software_label # MANDATORY: Provide the # framecode for software applications # used to derive the conformers and # identify other features such # secondary structure. Information # about the software application must # be given in save frames defined # above (see Section 6.). _Software_protocol_file_name # Optional: Enter the file # name as a value for this data # tag and submit the file with # the deposition form. _Software_parameter_file_name # Optional: Enter the file # name as a value for this data # tag and submit the file with # the deposition form. @ @ @ stop_ # Structural statistics for NMR structures derived by simulated # annealing or restrained molecular dynamics. The following data tags are # intended to capture the information in structure statistics tables appearing # in the literature. A '_Details' data tag is provided for authors to # include any necessary text to described the information in the list of data # tags and how it was derived. This would be the equivalent to the table # legend in a manuscript. # rms deviation from experimental distance constraints _Conformer_ensemble_intraresidue_distance_rms_dev @ _Conformer_ensemble_intraresidue_distance_rms_dev_error @ _Conformer_ensemble_sequential_rms_dev @ _Conformer_ensemble_sequential_rms_dev_error @ _Conformer_ensemble_short_range_rms_dev @ _Conformer_ensemble_short_range_rms_dev_error @ _Conformer_ensemble_long_range_rms_dev @ _Conformer_ensemble_long_range_rms_dev_error @ _Conformer_ensemble_unambiguous_inter-molecular_rms_dev @ _Conformer_ensemble_unambiguous_inter-molecular_rms_dev_error @ _Conformer_ensemble_ambiguous_inter-molecular_rms_dev @ _Conformer_ensemble_ambiguous_inter-molecular_rms_dev_error @ _Conformer_ensemble_ambiguous_intra-molecular_rms_dev @ _Conformer_ensemble_ambiguous_intra-molecular_rms_dev_error @ _Conformer_ensemble_hydrogen_bond_rms_dev @ _Conformer_ensemble_hydrogen_bond_rms_dev_error @ _Conformer_ensemble_dihedral_angles_rms_dev @ _Conformer_ensemble_dihedral_angles_rms_dev_error @ _Conformer_ensemble_dipolar_1H-1H_coupling_rms_dev @ _Conformer_ensemble_dipolar_1H-1H_coupling_rms_dev_error @ _Conformer_ensemble_dipolar_1H-15N_coupling_rms_dev @ _Conformer_ensemble_dipolar_1H-15N_coupling_rms_dev_error @ _Conformer_ensemble_dipolar_1H-13C_coupling_rms_dev @ _Conformer_ensemble_dipolar_1H-13C_coupling_rms_dev_error @ _Conformer_ensemble_dipolar_13C-13C_coupling_rms_dev @ _Conformer_ensemble_dipolar_13C-13C_coupling_rms_dev_error @ # potential energies _Conformer_ensemble_total_energy @ _Conformer_ensemble_total_energy_error @ _Conformer_ensemble_bond_energy @ _Conformer_ensemble_bond_energy_error @ _Conformer_ensemble_angle_energy @ _Conformer_ensemble_angle_energy_error @ _Conformer_ensemble_improper_energy @ _Conformer_ensemble_improper_energy_error @ _Conformer_ensemble_van_der_Waals_energy @ _Conformer_ensemble_van_der_Waals_energy_error @ _Conformer_ensemble_NOE_energy @ _Conformer_ensemble_NOE_energy_error @ _Conformer_ensemble_torsional_angle_potential_energy @ _Conformer_ensemble_torsional_angle_potential_energy_error @ _Conformer_ensemble_noncrystallographic_symmetry_potential_energy @ _Conformer_ensemble_noncrystallographic_symmetry_potential_energy_error @ _Conformer_ensemble_Lennard-Jones_potential_energy @ _Conformer_ensemble_Lennard-Jones_potential_energy_error @ # deviations from idealized geometries _Conformer_ensemble_covalent_bond_rms_dev @ _Conformer_ensemble_covalent_bond_rms_dev_error @ _Conformer_ensemble_bond_angle_rms_dev @ _Conformer_ensemble_bond_angle_rms_dev_error @ _Conformer_ensemble_impropers_rms_dev @ _Conformer_ensemble_impropers_rms_dev_error @ _Conformer_ensemble_peptide_planarity_rms_dev @ _Conformer_ensemble_peptide_planarity_rms_dev_error @ # Values for a representative conformer _Representative_conformer_intraresidue_distance_rms_dev @ _Representative_conformer_sequential_rms_dev @ _Representative_conformer_short_range_rms_dev @ _Representative_conformer_long_range_rms_dev @ _Representative_conformer_unambiguous_inter-molecular_rms_dev @ _Representative_conformer_ambiguous_inter-molecular_rms_dev @ _Representative_conformer_ambiguous_intra-molecular_rms_dev @ _Representative_conformer_hydrogen_bond_rms_dev @ _Representative_conformer_dihedral_angles_rms_dev @ _Representative_conformer_dipolar_1H-1H_coupling_rms_dev @ _Representative_conformer_dipolar_1H-13C_coupling_rms_dev @ _Representative_conformer_dipolar_1H-15N_coupling_rms_dev @ _Representative_conformer_dipolar_13C-13C_coupling_rms_dev @ _Representative_conformer_total_energy @ _Representative_conformer_bond_energy @ _Representative_conformer_angle_energy @ _Representative_conformer_improper_energy @ _Representative_conformer_van_der_Waals_energy @ _Representative_conformer_NOE_energy @ _Representative_conformer_torsional_angle_potential_energy @ _Representative_conformer_noncrystallographic_symmetry_potential_energy @ _Representative_conformer_Lennard-Jones_potential_energy @ _Representative_conformer_covalent_bond_rms_dev @ _Representative_conformer_bond_angle_rms_dev @ _Representative_conformer_impropers_rms_dev @ _Representative_conformer_peptide_planarity_rms_dev @ _Statistical_structure_parameter_details # Text description ; @ ; # Total distance constraint violation statistics: # Please indicate the way in which the violation statistics have been # calculated (i.e., over all distance constraints or calculated for # the violations only). _Distance_constraint_violation_stat_calc_method # MANDATORY # text entry ; @ ; _Maximum_distance_constraint_violation # MANDATORY @ # Absolute value _Average_distance_constraint_violation # MANDATORY @ # Calculated from # the absolute # values _RMSD_over_all_distance_constraint_violations # MANDATORY @ _Maximum_upper_distance_constraint_violation # Optional @ _Maximum_lower_distance_constraint_violation # Optional @ _Representative_conformer_maximum_upper_distance_bound_violation @ # Total angle constraint violation statistics: # Please indicate the way in which the violation statistics have been # calculated (i.e., over all angle constraints or calculated for the # violations only). # Values for the following angle constraint statistics data tag are # MANDATORY if angle constraints have been used in deriving the # reported family of conformers. _Torsion_angle_constraint_stat_calc_method # MANDATORY, text ; # entry @ ; _Maximum_torsion_angle_constraint_violation # MANDATORY @ # Absolute value _Average_torsion_angle_constraint_violation # MANDATORY @ # Calculated from # the absolute # values _Std_dev_over_all_torsion_angle_constraint_violations # MANDATORY @ # Total constraint violations: _Average_constraints_per_residue # MANDATORY @ _Average_constraint_violations_per_residue # MANDATORY @ # The next several data tags can be used to report statistics on the # heavy atom coordinates for the ensemble of conformers. If all # residues are not included in the statistical calculation, it is # important to indicate those that have been included. Also, indicate # how the statistics are calculated (i.e. pairwise, pairwise from the # mean, or pairwise from the average minimized structure. _Atom_coord_avg_rmsd_calc_method # MANDATORY # Text comment ; @ ; _Backbone_heavy_atom_residues_included # MANDATORY @ # character string # Example: [e.g.: '5-86'] _Backbone_heavy_atom_coord_avg_rmsd # MANDATORY @ _Backbone_heavy_atom_coord_std_dev # MANDATORY @ _Sidechain_heavy_atom_residues_included # MANDATORY, if true @ # character string # Example: [e.g.: '5-86'] _Sidechain_heavy_atom_coord_avg_rmsd # MANDATORY @ _Sidechain_heavy_atom_coord_std_dev # MANDATORY @ _All_heavy_atom_residues_included # MANDATORY @ # character string # Example: [e.g.: '5-86'] _All_heavy_atom_coord_avg_rmsd # MANDATORY @ _All_heavy_atom_coord_std_dev # MANDATORY @ # Where the agreement of the conformers with constraints or direct # spectroscopic data has been determined using a computational method, # please provide the value obtained and the functional form. _Struct_figure_of_merit # Optional @ _Struct_figure_of_merit_func_form # Optional @ #[e.g.: direct; 'r^6 # weighted'] save_ ####################################### # 13.1.1. Angular order parameters # ####################################### # Angular order parameters can be listed using the following saveframe. save_angular_order_parameters _Saveframe_category angular_order_parameters _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; loop_ _Residue_seq_code _Phi_S_angle_value _Psi_S_angle_value _Chi_one_S_angle_value _Chi_two_S_angle_value @ @ @ @ @ stop_ save_ ######################################## # 13.2. Constraint value statistics # ######################################## save_constraint_statistics _Saveframe_category constraint_statistics loop_ _Constraint_list_label # Provide the saveframe codes for the # constraint lists used to compile # the following statistics. @ stop_ _Text_data_format # If known the format for the data # provided in the 'text_data' field @ # [e.g.: 'ASCII comma delimited'] _Text_data # Used for data provided in a # non-standard format ; @ ; # For the following NOE, ROE and dipolar coupling data tags, sequential is # defined as |i-j| = 1, medium range is defined as 1<|i-j|<=5 and long range # as |i-j|>5 where i and j are the residue numbers. ################################### # 13.2.1. NOE values (proteins) # ################################### _NOE_constraints_total_count @ _NOE_intraresidue_constraints_total_count @ _NOE_sequential_constraints_total_count @ _NOE_medium_range_constraints_total_count @ _NOE_long_range_constraints_total_count @ _NOE_unambiguous_intermolecular_constraints_total_count @ _NOE_ambiguous_intramolecular_constraints_total_count @ _NOE_ambiguous_intermolecular_constraints_total_count @ ################################### # 13.2.2. ROE values (proteins) # ################################### _ROE_constraints_total_count @ _ROE_intraresidue_constraints_total_count @ _ROE_sequential_constraints_total_count @ _ROE_medium_range_constraints_total_count @ _ROE_long_range_constraints_total_count @ _ROE_unambiguous_intermolecular_constraints_total_count @ _ROE_ambiguous_intramolecular_constraints_total_count @ _ROE_ambiguous_intermolecular_constraints_total_count @ ######################################################### # 13.2.3. Methods used to quantify NOE and ROE values # ######################################################### # Each of the following six data tags is provided so that the author # can give a brief text description of the method used to quantify the # reported constraints. _NOE_interproton_distance_evaluation # Optional text description ; @ ; _NOE_pseudoatom_corrections # Optional text description ; @ ; _NOE_motional_averaging_correction # Optional text description ; @ ; _ROE_interproton_distance_evaluation # Optional text description ; @ ; _ROE_pseudoatom_corrections # Optional text description ; @ ; _ROE_motional_averaging_correction # Optional text description ; @ ; ############################################ # 13.2.4. Dipolar coupling constraints # ############################################ _Dipolar_constraints_calibration_method ; @ ; _Molecular_align_tensor_axial_symmetric_component @ _Molecular_align_tensor_rhombic_component @ _Generalized_order_parameter_for_internal_motions_S @ _Assumed_proton_nitrogen_bond_length @ _Assumed_proton_carbon_bond_length @ _Assumed_carbon_nitrogen_bond_length @ _Dipolar_constraints_total_count @ _Dipolar_constraints_1H_1H_total_count @ _Dipolar_constraints_1H_13C_total_count @ _Dipolar_constraints_1H_15N_total_count @ _Dipolar_constraints_13C_13C_total_count @ _Dipolar_constraints_13C_15N_total_count @ _Dipolar_intraresidue_constraints_total_count @ _Dipolar_sequential_constraints_total_count @ _Dipolar_medium_range_constraints_total_count @ _Dipolar_long_range_constraints_total_count @ _Dipolar_unambiguous_intermolecular_constraints_total_count @ _Dipolar_ambiguous_intramolecular_constraints_total_count @ _Dipolar_ambiguous_intermolecular_constraints_total_count @ ################################################## # 13.2.5. Torsion angle constraints (proteins) # ################################################## _Protein_phi-angle_constraints_total_count @ _Protein_psi-angle_constraints_total_count @ _Protein_chi_one-angle_constraints_total_count @ _Protein_other_angle_constraints_total_count @ ################################################################# # 13.2.6. Torsion angle and other constraints (nucleic acids) # ################################################################# _NA_beta-angle_constraints_total_count @ _NA_gamma-angle_constraints_total_count @ _NA_delta-angle_constraints_total_count @ _NA_epsilon-angle_constraints_total_count @ _NA_chi-angle_constraints_total_count @ _NA_sugar_pucker_constraints_total_count @ _NA_other_angle_constraints_total_count @ ######################################## # 13.2.7. Hydrogen bond constraints # ######################################## _Hydrogen_bonds_constrained_total_count @ _Constraints_defining_hydrogen_bonds_total_count @ ######################################## # 13.2.8. Disulfide bond constraints # ######################################## _Disulfide_bonds_constrained_total_count @ _Constraints_defining_disulfide_bonds_total_count @ ################################ # 13.2.9. Other constraints # ################################ _Derived_coupling_constant_constraints_total_count @ _Derived_chemical_shift_constraints_total_count @ _Derived_photo_cidnp_constraints_total_count @ _Derived_paramagnetic_relaxation_constraints_total_count @ _Assumed_distance_constraints_total_count @ _Assumed_angle_constraints_total_count @ save_ ################################ # 13.3. Structure features # ################################ # This section is used to summarize structural features present in the # structure of the molecular system studied. ################################## # 13.3.1. Secondary structure # ################################## save_secondary_structure_features _Saveframe_category secondary_structure_features loop_ _Selection_method # Method used to select the secondary # structure features. @ stop_ loop_ _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Beginning_residue_seq_code # MANDATORY [e.g.: 45] _Last_residue_seq_code # MANDATORY [e.g.: 52] _Secondary_structure_name # MANDATORY [e.g.: 'helix a'; 'helix b'] _Secondary_structure_type # MANDATORY [e.g.: alpha-helix; # '3-10 helix'; beta-sheet; turn; loop] _Selection_method # [e.g.: author-determined] _Details @ @ @ @ @ @ ; @ ; stop_ save_ ########################################## # 13.3.2. Tertiary structure elements # ########################################## save_tertiary_structure_elements _Saveframe_category tertiary_structure_elements _Selection_method ; @ ; loop_ _Citation_label @ stop_ loop_ _Tertiary_structure_element_ID _Tertiary_structure_code # [e.g.: 'active site'] _Mol_system_component_name _Residue_seq_code _Residue_label _Atom_name _Details @ @ @ @ @ @ ; @ ; stop_ save_ ############################################################# # 13.3.3. Covalent and other types of bonds and linkages # ############################################################# ############################### # 13.3.3.1. Hydrogen bonds # ############################### save_hydrogen_bonds _Saveframe_category hydrogen_bonds _Selection_method ; @ ; loop_ _Hydrogen_bond_ID _Heavy_atom_one_mol_system_component_name # MANDATORY; [e.g.: # ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Heavy_atom_one_residue_seq_code # MANDATORY _Heavy_atom_one_residue_label # MANDATORY _Heavy_atom_one_atom_name # MANDATORY _Hydrogen_atom_name # MANDATORY _Heavy_atom_two_mol_system_component_name # MANDATORY _Heavy_atom_two_residue_seq_code # MANDATORY _Heavy_atom_two_residue_label # MANDATORY _Heavy_atom_two_atom_name # MANDATORY _Details @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Observed_conformer_hydrogen_bond_ID _Observed_conformer_ID @ @ stop_ save_ ################################ # 13.3.3.2. Disulfide bonds # ################################ save_disulfide_bonds _Saveframe_category disulfide_bonds _Selection_method ; @ ; loop_ _Disulfide_bond_ID _Disulfide_bond_conformation # [e.g.: right-hand; left-hand] _Residue_one_mol_system_component_name _Residue_one_residue_seq_code _Residue_one_residue_label _Residue_two_mol_system_component_name _Residue_two_residue_seq_code _Residue_two_residue_label _Details @ @ @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Observed_conformer_disulfide_bond_ID _Observed_conformer_ID @ @ stop_ save_ ################################# # 13.3.3.3. Bonds to ligands # ################################# save_ligand_bonds _Saveframe_category ligand_bonds _Selection_method ; @ ; loop_ _Ligand_bond_ID _Residue_mol_system_component_name _Residue_seq_code _Residue_label _Residue_atom_label _Ligand_mol_system_component_name _Ligand_atom_label _Details @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Observed_conformer_ligand_bond_ID _Observed_conformer_ID @ @ stop_ save_ ############################# # 13.3.3.4. Salt bridges # ############################# save_salt_bridges _Saveframe_category salt_bridges _Selection_method ; @ ; loop_ _Salt_bridge_ID _Salt_bridge_atom_one_mol_system_component_name # MANDATORY; [e.g.: # ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Salt_bridge_atom_one_residue_seq_code # MANDATORY _Salt_bridge_atom_one_residue_label # MANDATORY _Salt_bridge_atom_two_mol_system_component_name # MANDATORY _Salt_bridge_atom_two_residue_seq_code # MANDATORY _Salt_bridge_atom_two_residue_label # MANDATORY _Details @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Observed_conformer_salt_bridge_ID _Observed_conformer_ID @ @ stop_ save_ ##################################### # 13.3.3.5. Other types of links # ##################################### save_ _Saveframe_category other_links _Selection_method ; @ ; loop_ _Link_ID _Link_type # Descriptive name for linkage _Link_atom_one_mol_system_component_name # MANDATORY; [e.g.: # ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Link_atom_one_residue_seq_code # MANDATORY _Link_atom_one_residue_label # MANDATORY _Link_atom_one_atom_name # MANDATORY _Link_atom_two_mol_system_component_name # MANDATORY _Link_atom_two_residue_seq_code # MANDATORY _Link_atom_two_residue_label # MANDATORY _Link_atom_two_atom_name # MANDATORY _Details @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Observed_conformer_link_ID _Observed_conformer_ID @ @ stop_ save_ ################################## # 13.3.3.6. Cis peptide bonds # ################################## save_cis_peptide_bonds _Saveframe_category cis_peptide_bonds _Selection_method ; @ ; loop_ _Cis_peptide_bond_ID _Mol_system_component_name _Residue_one_residue_seq_code _Residue_two_residue_seq_code @ @ @ @ stop_ loop_ _Observed_conformer_cis_peptide_bond_ID _Observed_conformer_ID @ @ stop_ save_ ####################################### # 13.3.4. Other structure features # ####################################### save_ _Saveframe_category other_structure_features _Details ; @ ; _Selection_method ; @ ; loop_ _Mol_system_component_name _Residue_seq_code @ @ stop_ save_ ############################################################## # 13.4. Atomic coordinates for a representative conformer # ############################################################## # The atomic coordinates for a structure representative of the set of # calculated conformers is entered in the next section. Data are # entered here only if this structure is not identical to one of the # conformers entered above or provided in an auxiliary file. # This save frame is not needed if the coordinates for a minimized average # structure or similar structure representative of the conformers # determined in this study are provided in an auxiliary file identified # with the data tag '_Min_avg_structure_file_name'. save_ _Saveframe_category representative_structure _Details ; @ ; _Rep_structure_derivation # MANDATORY (text ; # description of methods used to @ # calculate the reported ; # representative structure.) _Rep_structure_file_name # Name of the file attached to this @ # submission that contains the atomic # coordinates in PDB format for a # minimized average structure or # similar structure determined for # the system. _Rep_structure_original_file # Filename supplied by BMRB for @ # original data submitted by the author # For PDB entries the terminal residue for each molecular chain in the # structure must be defined. This can be accomplished using the following # loop_. loop_ _Terminal_residue_mol_system_component_name _Terminal_residue_residue_seq_code _Terminal_residue_residue_label @ @ @ stop_ _Structure_coordinate_set_label # $framecode for the set of ; # conformers that define the @ # representative structure ; # reported in this save frame. loop_ _Atom_list_number # Optional: sequential numbering # of the atoms in the list # beginning with the number 1. _Mol_system_component_name # MANDATORY # [e.g.: A1; B2; H1; peptide; Cu] _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY _Atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_type # Optional [e.g.: H; C; N; O; S; P] _Atom_cartn_x # MANDATORY _Atom_cartn_y # MANDATORY _Atom_cartn_z # MANDATORY _Atom_pairwise_cartn_rmsd # Optional: The RMSD for the # cartesian coordinate positions # of the atom in the ensemble of # conformers. @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################################## # 13.5. Atomic coordinates for a family of structures # ########################################################## # A save frame like the following one must be provided for each unique # family of structures derived from the NMR data (e.g. two save frames # would be required if two unique families of structures are found to # fit the data). save_ _Saveframe_category structure_coordinate_set _Details # Optional descriptive comment ; # about the data. @ ; _Conformer_family_original_file_ID # Filename supplied by BMRB for @ # original data submitted by the author # It is mandatory that the software used to derive the structure (X- # PLOR, DGII, DYANA, etc.) be defined. Providing protocols and # parameter lists is optional. # The following loop is used to describe any unique energetic penalty # functions used in the reported structure determination. loop_ # Optional loop _Energetic_penalty_function _Energetic_penalty_function_description @ ; @ ; stop_ # List of framecodes where data used to derive the reported structures are # located. loop_ # MANDATORY _Applied_data_set_label # Listed here are the # framecodes for the save frames # containing quantitative # results used in determining # the reported conformers. # [e.g.: $chemical_shift_assignment_data_set_1; # $coupling_constant_data_set_1; # $homonuclear_NOE_data_set_1] @ stop_ # List of Experiments (NMR) used to generate the data in this saveframe. # This information is not needed here if the equivalent data has been # supplied in saveframes that have been listed in the loop_ immediately # above. loop_ # Optional Loop _Experiment_label # Framecodes for # experiments listed in Section 7. @ stop_ loop_ _Sample_label # MANDATORY [e.g.: $sample_one] @ # Framecode for a save frame defined # in Section 5.1 that best represents # the sample studied. stop_ _Sample_conditions_label # MANDATORY @ # [e.g.: $sample_conditions_set_1 ] # (see Section 8, above) loop_ _Constraint_list_label # MANDATORY @ # Saveframe code for the saveframe # containing the constraints used to # calculate the family of structures # reported in this save frame [e.g.: # $constraint_set_1]. stop_ # The following loop can be used to provide the file name and format # for an image file that contains a view of the molecule's structure # in a particular orientation or an expanded view that the author # would like users to be able to display. A file containing the image # data must accompany the deposition form. loop_ # Optional loop _Structure_image_file_name _Structure_image_file_format # [e.g.: GIF; JPEG] _Structure_image_details # Text description of the image. @ @ ; @ ; stop_ _Conformer_file_name # Name of the file attached to this @ # submission that contains the atomic # coordinates in PDB format for all # of the conformers being submitted. _Constraints_original_file_ID # Filename supplied by BMRB for @ # original data submitted by the author # The following data does not need to be entered if they are provided in an # auxiliary file attached to the submission as defined above for the data # tag '_Conformer_file_name'. # Using this loop structure, enter the atomic coordinate and atom # identification information for the family of conformers that is # being submitted. # Molecules such as solvent or ions can be included in individual # model structures by providing a value for the _Mol_label data tag, # entering a unique value for the _Mol_component_name data tag, # and providing all values needed to identify uniquely the atom. # These molecules need to be listed as part of the system, and # do need to be described in save frames for non-polymers. # Example: _Mol_label [e.g.: $HOH; $Na; $Cl] # _Mol_component_name [e.g.: 1; 2; 3; 4] loop_ _Atom_list_number # MANDATORY (integer) _Conformer_number # MANDATORY (integer that # specifies the conformer) _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Residue_seq_code # Cond-MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Cond-MANDATORY (for polymers) # [e.g.: A; ala; Ala; ALA; G] _Atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_type # MANDATORY [e.g.: H; C; N; O; S; P] _Atom_cartn_x # MANDATORY _Atom_cartn_y # MANDATORY _Atom_cartn_z # MANDATORY @ @ @ @ @ @ @ @ @ @ stop_ ######################################################################### # # # Example: # # # # loop_ # # _Atom_list_number # # _Conformer_number # # _Mol_system_component_name # # _Residue_seq_code # # _Residue_label # # _Atom_type # # _Atom_name # # _Atom_cartn_x # # _Atom_cartn_y # # _Atom_cartn_z # # # # 1 1 BPTI 5 S N N 9.687 27.909 3.152 # # 2 1 BPTI 5 S H H 10.707 27.912 3.293 # # 3 1 BPTI 5 S C CA 9.124 28.168 1.840 # # 4 1 BPTI 5 S H HA 8.211 27.576 1.776 # # 5 1 BPTI 5 S C CB 8.778 29.648 1.642 # # 6 1 BPTI 5 S H HB2 8.172 29.776 0.745 # # 7 1 BPTI 5 S H HB3 8.246 30.030 2.513 # # 8 1 BPTI 5 S O OG 10.000 30.391 1.484 # # 9 1 BPTI 5 S H HG 10.793 29.822 1.812 # # 10 1 BPTI 5 S C C 10.108 27.719 0.765 # # 11 1 BPTI 5 S O O 11.332 27.660 1.047 # # # # stop_ # # # ######################################################################### save_ ################################## # 13.6. Structure constraints # ################################## ################################### # 13.6.1. Distance constraints # ################################### save_ _Saveframe_category distance_constraints loop_ _Atom_one_mol_system_component_name # Optional, needed for complex # and multimeric molecules. # [e.g.: A1; B2; H1; peptide; Cu] _Atom_one_residue_seq_code # MANDATORY [e.g.: 1; 2; 3; 4] _Atom_one_atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_atom_name # MANDATORY _Distance_value # Optional _Distance_upper_bound_value # MANDATORY _Distance_lower_bound_value # MANDATORY _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ @ stop_ save_ save_ _Saveframe_category distance_ambiguous_constraints loop_ # Reported ambiguous distance constraints _Constraint_list_ID _Related_constraint_list_ID _Atom_one_mol_system_component_name # Optional, needed for complex # and multimeric molecules. # [e.g.: A1; B2; H1; peptide; Cu] _Atom_one_residue_seq_code # MANDATORY [e.g.: 1; 2; 3; 4] _Atom_one_atom_name # MANDATORY [e.g.: HB3; HG11] _Atom_two_mol_system_component_name # Optional, needed for complex # and multimeric molecules. _Atom_two_residue_seq_code _Atom_two_atom_name # MANDATORY _Distance_value # Optional _Distance_upper_bound_value # MANDATORY _Distance_lower_bound_value # MANDATORY _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ###################################################### # 13.6.2. Constraints expressed as torsion angles # ###################################################### save_ _Saveframe_category torsion_angle_constraints _Mol_system_component_name # MANDATORY @ loop_ _Torsion_angle_name # [e.g.: phi; psi; chi1; omega] _Karplus_equation_citation_label # Cite the source for the # Karplus equation # coefficients. @ @ stop_ loop_ _Atom_one_residue_seq_code # MANDATORY _Atom_one_atom_name # MANDATORY _Atom_two_residue_seq_code # MANDATORY _Atom_two_atom_name # MANDATORY _Atom_three_residue_seq_code # MANDATORY _Atom_three_atom_name # MANDATORY _Atom_four_residue_seq_code # MANDATORY _Atom_four_atom_name # MANDATORY _Angle_upper_bound_value # MANDATORY _Angle_lower_bound_value # MANDATORY _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ############################################################ # 13.6.3. Combined CA and CB chemical shift constraints # ############################################################ save_ _Saveframe_category chem_shift_CA_CB_constraints _Mol_system_component_name # MANDATORY @ loop_ _List_number _Atom_one_residue_seq_code _Atom_one_atom_name _Atom_two_residue_seq_code _Atom_two_atom_name _Atom_three_residue_seq_code _Atom_three_atom_name _Atom_four_residue_seq_code _Atom_four_atom_name _Atom_five_residue_seq_code _Atom_five_atom_name _CA_chemical_shift_value _CB_chemical_shift_value _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 13.6.4. H chemical shift constraints # ########################################### save_ _Saveframe_category chem_shift_H_constraints _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] loop_ _List_number _Residue_seq_code _Atom_name _Chem_shift_value _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ stop_ save_ ####################################### # 13.6.5. J three bond constraints # ####################################### save_ _Saveframe_category J_three_bond_constraints loop_ _List_number _Atom_one_mol_system_component_name # MANDATORY _Atom_one_residue_seq_code _Atom_one_atom_name _Atom_two_mol_system_component_name # MANDATORY _Atom_two_residue_seq_code _Atom_two_atom_name _Atom_three_mol_system_component_name # MANDATORY _Atom_three_residue_seq_code _Atom_three_atom_name _Atom_four_mol_system_component_name # MANDATORY _Atom_four_residue_seq_code _Atom_four_atom_name _Coupling_constant_value _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 13.6.6. Dipolar coupling constraints # ########################################### save_ _Saveframe_category dipolar_coupling_constraints loop_ _List_number _Atom_one_mol_system_component_name # MANDATORY _Atom_one_residue_seq_code _Atom_one_atom_name _Atom_two_mol_system_component_name # MANDATORY _Atom_two_residue_seq_code _Atom_two_atom_name _Dipolar_coupling_value _Derivation_code # Optional _Source_experiment_label # Optional @ @ @ @ @ @ @ @ @ @ stop_ save_ ################################ # 13.6.7. Other constraints # ################################ save_ _Saveframe_category other_constraints _Mol_system_component_name # MANDATORY; [e.g.: ribonuclease; @ # 'plastocyanin peptide'; # 'DNA strand 1'; A1; B2; H1] _Constraint_other_type # Something that does not fit # the above categories. ; @ ; _Constraint_other_software_format # Name of the software whose # format in which the # constraints are provided. ' @ ' _Constraint_other_list # list of constraints provided # as a text file ; @ ; save_ ########################## # 13.7. Raw data file # ########################## save_expt_NMR_primary_data _Saveframe_category NMR_primary_data _Atomic_coordinate_set_label @ _Expt_NMR_primary_data_file_name # Optional: Name of a file # containing the raw data for an @ # NOE or ROE NMR experiment # representative of the data # used to determine the # structure. This file, if # provided, is not expected to # be an ASCII text file, but a # binary file retrieved directly # from the spectrometer. save_ ################################### # 13.8. Atom nomenclature maps # ################################### # This section is used to specify the correlation between the atom # nomenclature used for the constraint input data and the atom # nomenclature reported for the conformers. The IUPAC # nomenclature for side-chain atoms attached to atoms that have a # planer geometry is dependent on the cis/trans orientation of the # side-chain atom. This applies to the side-chains of Asp, Glu, Arg, # Phe, and Tyr. Because the conformation of the side-chain may differ # between individual structures in a family of structures, the # constraint input data assigned to an atom with a defined name (Tyr # HD1) may in one structure correspond to the HD1 atom and in another # to the HD2 atom. To be able to correctly relate the constraint data # to atoms in the derived structures a map is needed to correlate the # assigned constraints with atoms in the derived conformers. # Only atoms with conformational dependent nomenclature and # discrepancies between their derived name and the name assigned to # the constraint data need to be listed in the following loops. # Note: Several structure validation software packages may reassign # the names given specific atoms on the basis of their conformation in # a structure. In addition, the PDB does not follow IUPAC # nomenclature and will change atom names such as HB2 and HB3 to HB1 # and HB2, respectively. save_ _Saveframe_category conformer_atom_nom_map _Structure_coordinate_set_label @ loop_ _Conformer_number _Mol_system_component_name # MANDATORY, needed for complex # molecules. # [e.g.: A1; B2; H1; peptide; Cu] _Residue_seq_code # MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Optional _Atom_name_input_data # MANDATORY [e.g.: HB3; HG11] _Atom_name_alternate # MANDATORY @ @ @ @ @ @ stop_ save_ save_ _Saveframe_category rep_struct_atom_nom_map _Structure_coordinate_set_label @ _Representative_structure_label @ loop_ _Mol_system_component_name # MANDATORY # [e.g.: A1; B2; H1; peptide; Cu] _Residue_seq_code # MANDATORY [e.g.: 1; 2; 3; 4] _Residue_label # Optional _Atom_name_input_data # MANDATORY [e.g.: HB3; HG11] _Atom_name_alternate # MANDATORY @ @ @ @ @ stop_ save_ ########################################### # 16. Cited references within the entry # ########################################### # As in a journal article, authors may wish to include references to # previously published or related data, pulse sequences, experimental # protocols, etc. These references are listed here by creating and # completing a save frame like the following one for each individual # reference. The framecode (e.g., $citation_1) is then inserted # as a value for a citation data tag(s) in earlier sections of the # deposition. save_ # Optional save frame # Repeat the save frame and provide a unique label for # each citation. The label is used in the above # saveframes in the same manner as a reference in a # journal article. # Examples: [save_citation_one; save_citation_1] _Saveframe_category citation # Using the data tag given below enter the full reference in a format # consistent with a journal reference. _Citation_full ; @ ; save_