BMRB Data Deposition Form Version 2.1 Full Form for Assigned Chemical Shifts and Coupling Constants from Simple Molecular Systems ################## # 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_ ########################### # 1. Entry information # ########################### save_entry_information _Saveframe_category entry_information _Entry_title ; @ ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title @ @ @ @ @ stop_ _Entry_type @ _Entry_origination @ _NMR_STAR_version 2.1 _Experimental_method @ _Details ; @ ; _Special_processing_instructions ; @ ; loop_ _Related_BMRB_accession_number _Relationship @ @ stop_ _Revised_BMRB_accession_number @ _Replace_BMRB_accession_number @ _Revision_details ; @ ; _Release_immediately @ _Release_on_publication @ _Release_date_request @ _Release_date_justification ; @ ; save_ ######################### # 2. Contact persons # ######################### save_contact_persons _Saveframe_category contact_persons loop_ _Family_name _Given_name _Middle_initials _Family_title _Department_and_Institution _Mailing_address _Phone_number _Email_address _FAX_number @ @ @ @ ; @ ; ; @ ; @ @ @ @ @ @ @ ; @ ; ; @ ; @ @ @ 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 # ################################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; @ ; _Citation_status @ _Citation_type @ loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title @ @ @ @ @ stop_ _Journal_abbreviation @ _Journal_name_full @ _Journal_volume @ _Journal_issue @ _Book_title @ _Book_chapter_title @ _Book_volume @ _Book_series @ _Book_publisher @ _Book_publisher_city @ _Conference_title @ _Conference_site @ _Conference_state_province @ _Conference_country @ _Conference_start_date @ _Conference_end_date @ _Conference_abstract_number @ _Thesis_institution @ _Thesis_institution_city @ _Thesis_institution_country @ _Page_first @ _Page_last @ _Year @ _Details ; @ ; loop_ _Keyword @ stop_ loop_ _Editor_ordinal _Editor_family_name _Editor_given_name _Editor_middle_initials _Editor_family_title @ @ @ @ @ stop_ save_ ###################################### # 4. Molecular system description # ###################################### save_ _Saveframe_category molecular_system _Mol_system_name @ _Abbreviation_common @ _Enzyme_commission_number @ loop_ _Mol_system_component_name _Mol_label @ @ stop_ _System_molecular_weight @ _System_physical_state @ _System_oligomer_state @ _System_type @ _System_paramagnetic @ loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component @ @ stop_ loop_ _Biological_function @ stop_ loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_relation_type _Database_entry_details PDB @ @ @ ; @ ; CATH @ @ @ ; @ ; SCOP @ @ @ ; @ ; stop_ _Details ; @ ; save_ ############################# # 4.1. Monomeric polymers # ############################# save_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class @ _Name_common @ _Name_variant @ _Abbreviation_common @ _Name_CAS @ _CAS_registry_number @ _Enzyme_commission_number @ _Molecular_mass @ loop_ _Biological_function @ stop_ _Details ; @ ; loop_ _Synonym @ stop_ ####################################### # 4.1.1. Polymer residue sequence # ####################################### _Sequence_citation_label @ _Ambiguous_sequence_features ; @ ; _Residue_count @ _Mol_residue_sequence ; @ ; loop_ _Residue_seq_code _Residue_author_seq_code _Insertion_code _Residue_label _Segment_definition_code @ @ @ @ @ stop_ loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_segment_ID _Sequence_homology_type _Sequence_difference_details _Sequence_alignment_details GenBank @ @ @ @ ; @ ; ; @ ; SWISS-PROT @ @ @ @ ; @ ; ; @ ; PIR @ @ @ @ ; @ ; ; @ ; PDB @ @ @ @ ; @ ; ; @ ; stop_ save_ ############################################### # 4.4. Molecular bond linkage definitions # ############################################### save_crosslink_bond_definitions _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name _Details @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ loop_ _Deleted_atom_mol_system_component_name _Deleted_atom_residue_seq_code _Deleted_atom_residue_label _Deleted_atom_name @ @ @ @ stop_ save_ ########################## # 4.6. Natural source # ########################## save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _Organism_acronym _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain _Variant _Subvariant _Organ _Tissue _Cell_line _Cell_type _ATCC_number _Organelle _Fraction _Secretion _Plasmid _Gene_mnemonic _Details @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ ; @ ; 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 # ################################ save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Variant _Organ _Tissue _Cell_line _Cell_type _ATCC_number _Vector_type _Vector_name _Vendor_name _Gene_source _Details @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ ; @ ; stop_ save_ ######################################### # 5. Sample contents and methodology # ######################################### ############################## # 5.1. Sample description # ############################## save_ _Saveframe_category sample _Sample_type @ _Details ; @ ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling @ @ @ @ @ @ stop_ ########################################################################## # 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]' # # # ########################################################################## save_ ################################### # 5.2. Purity of the molecules # ################################### save_sample_mol_purity _Saveframe_category sample_mol_purity _Details ; @ ; _Sample_label @ loop_ _Mol_label _Mol_purity_value _Mol_purity_value_units _Mol_purity_measurement_method @ @ @ @ stop_ save_ ################################ # 6. Computer software used # ################################ save_ _Saveframe_category software _Name @ _Version @ loop_ _Vendor _Address _Electronic_address @ ; @ ; @ stop_ loop_ _Task @ stop_ loop_ _Platform_vendor _Platform_model _Operating_system _Operating_system_version _Hardware_code @ @ @ @ @ stop_ _Citation_label @ save_ ############################# # 7. Experimental detail # ############################# ######################################## # 7.1. NMR Spectrometer definitions # ######################################## save_ _Saveframe_category NMR_spectrometer _Manufacturer @ _Model @ _Field_strength @ _Software_version_number @ _Details ; @ ; save_ #################################### # 7.2. NMR applied experiments # #################################### save_ _Saveframe_category NMR_applied_experiment _Experiment_name @ _Sample_label @ _BMRB_pulse_sequence_accession_number @ _Pulse_sequence_file_name @ _Pulse_sequence_parameter_file_name @ _Pulse_sequence_schematic_file_name @ _Pulse_sequence_schematic_file_format @ loop_ _Citation_label @ stop_ _Details ; @ ; ################################################# # 7.2.1. NMR spectral acquisition parameters # ################################################# loop_ _Acquisition_dimension_ID _Detected_atom_type _Spectrometer_carrier_frequency _Acquisition_time _Mixing_time _Spectral_width _Spectral_folding _Data_point_number _Data_point_type _Data_point_spacing @ @ @ @ @ @ @ @ @ @ stop_ ################################################ # 7.2.2. NMR spectral processing parameters # ################################################ loop_ _Processing_dimension_ID _Exponential_factor _Gaussian_factor _Processed_real_points @ @ @ @ stop_ save_ ########################### # 8. Sample conditions # ########################### save_ _Saveframe_category sample_conditions _Details ; @ ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_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_ _Saveframe_category chemical_shift_reference _Details ; @ ; loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio _Indirect_shift_ratio_citation_label _Reference_correction_type _Correction_value _Correction_value_citation_label @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 9.1.2. Assigned chemical shift lists # ########################################### ################################################################### # 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 ; @ ; loop_ _Software_label @ stop_ loop_ _Experiment_label @ stop_ loop_ _Sample_label @ stop_ _Sample_conditions_label @ _Chem_shift_reference_set_label @ _Mol_system_component_name @ _Text_data_format @ _Text_data ; @ ; loop_ _Nucleus _Chemical_shift_error 1H @ 2H @ 3H @ 13C @ 15N @ 19F @ 31P @ stop_ loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code @ @ @ @ @ @ @ @ stop_ loop_ _Atom_shift_assign_ID_ambiguity @ stop_ save_ ############################# # 9.2. Coupling constants # ############################# save_ _Saveframe_category coupling_constants _Details ; @ ; loop_ _Software_label @ stop_ loop_ _Experiment_label @ stop_ loop_ _Sample_label @ stop_ _Sample_conditions_label @ _Spectrometer_frequency_1H @ _Mol_system_component_name @ _Text_data_format @ _Text_data ; @ ; loop_ _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error @ @ @ @ @ @ @ @ @ @ @ stop_ save_ ########################################### # 10. Cited references within the entry # ########################################### save_ _Saveframe_category citation _Citation_full ; @ ; save_