BMRB Entry 15651
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15651
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Title: NMR structure of the transmembrane domain of the Outer Membrane Protein A from Klebsiella pneumoniae in DHPC micelles. PubMed: 18952100
Deposition date: 2008-02-04 Original release date: 2008-11-04
Authors: Renault, Marie; Saurel, Olivier; Gervais, Virginie; Lohr, Franck; Reat, Valerie; Piotto, Martial; Milon, Alain
Citation: Renault, Marie; Saurel, Olivier; Czaplicki, Jerzy; Demange, Pascal; Gervais, Virginie; Lohr, Frank; Reat, Valerie; Piotto, Martial; Milon, Alain. "Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications" J. Mol. Biol. 385, 117-130 (2009).
Assembly members:
KpOmpA_transmembrane_domain, polymer, 216 residues, 23367.7 Da.
Natural source: Common Name: Klebsiella pneumoniae Taxonomy ID: 573 Superkingdom: Bacteria Kingdom: not available Genus/species: Klebsiella pneumoniae
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
KpOmpA_transmembrane_domain: ARIMKAIFVLNAAPKDNTWY
AGGKLGWSQYHDTGFYGNGF
QNNNGPTRNDQLGAGAFGGY
QVNPYLGFEMGYDWLGRMAY
KGSVDNGAFKAQGVQLTAKL
GYPITDDLDIYTRLGGMVWR
ADSKGNYASTGVSRSEHDTG
VSPVFAGGVEWAVTRDIATR
LEYQWVNNIGDAGTVGTRPD
NGMLSLGVSYRFGQEDAAPV
VAPAPAPAPEHHHHHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 673 |
| 15N chemical shifts | 170 |
| 1H chemical shifts | 359 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | KpOmpA transmembrane domain | 1 |
Entities:
Entity 1, KpOmpA transmembrane domain 216 residues - 23367.7 Da.
Residues 1-3 represent a non-native cloning tag and residues 211-216 represent a non-native affinity tag.
| 1 | ALA | ARG | ILE | MET | LYS | ALA | ILE | PHE | VAL | LEU | ||||
| 2 | ASN | ALA | ALA | PRO | LYS | ASP | ASN | THR | TRP | TYR | ||||
| 3 | ALA | GLY | GLY | LYS | LEU | GLY | TRP | SER | GLN | TYR | ||||
| 4 | HIS | ASP | THR | GLY | PHE | TYR | GLY | ASN | GLY | PHE | ||||
| 5 | GLN | ASN | ASN | ASN | GLY | PRO | THR | ARG | ASN | ASP | ||||
| 6 | GLN | LEU | GLY | ALA | GLY | ALA | PHE | GLY | GLY | TYR | ||||
| 7 | GLN | VAL | ASN | PRO | TYR | LEU | GLY | PHE | GLU | MET | ||||
| 8 | GLY | TYR | ASP | TRP | LEU | GLY | ARG | MET | ALA | TYR | ||||
| 9 | LYS | GLY | SER | VAL | ASP | ASN | GLY | ALA | PHE | LYS | ||||
| 10 | ALA | GLN | GLY | VAL | GLN | LEU | THR | ALA | LYS | LEU | ||||
| 11 | GLY | TYR | PRO | ILE | THR | ASP | ASP | LEU | ASP | ILE | ||||
| 12 | TYR | THR | ARG | LEU | GLY | GLY | MET | VAL | TRP | ARG | ||||
| 13 | ALA | ASP | SER | LYS | GLY | ASN | TYR | ALA | SER | THR | ||||
| 14 | GLY | VAL | SER | ARG | SER | GLU | HIS | ASP | THR | GLY | ||||
| 15 | VAL | SER | PRO | VAL | PHE | ALA | GLY | GLY | VAL | GLU | ||||
| 16 | TRP | ALA | VAL | THR | ARG | ASP | ILE | ALA | THR | ARG | ||||
| 17 | LEU | GLU | TYR | GLN | TRP | VAL | ASN | ASN | ILE | GLY | ||||
| 18 | ASP | ALA | GLY | THR | VAL | GLY | THR | ARG | PRO | ASP | ||||
| 19 | ASN | GLY | MET | LEU | SER | LEU | GLY | VAL | SER | TYR | ||||
| 20 | ARG | PHE | GLY | GLN | GLU | ASP | ALA | ALA | PRO | VAL | ||||
| 21 | VAL | ALA | PRO | ALA | PRO | ALA | PRO | ALA | PRO | GLU | ||||
| 22 | HIS | HIS | HIS | HIS | HIS | HIS |
Samples:
sample_1: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%
sample_2: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%
sample_3: KpOmpA transmembrane domain, [U-15N; 10% 13C], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%
sample_4: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 313 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D [15N,1H]-TROSY | sample_1 | isotropic | sample_conditions_1 |
| 3D [15N,1H]-TROSY-HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D [15N,1H]-TROSY-HN(CO)CACB | sample_1 | isotropic | sample_conditions_1 |
| 3D [15N,1H]-TROSY-HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D [15N,1H]-TROSY-HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D (HNCA)CC-TOCSY-(CA)-[15N,1H]-TROSY | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)C(CC)-TOCSY-(CA)-[15N,1H]-TROSY | sample_2 | isotropic | sample_conditions_1 |
| 3D H(CCCO)-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D [1H,13C]-CT-HSQC | sample_3 | isotropic | sample_conditions_1 |
| 4D 15N,15N-separated HMQC-NOESY-TROSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N,13C-separated HMQC-NOESY-TROSY | sample_4 | isotropic | sample_conditions_1 |
| 3D 13C,13C-separated HMQC-NOESY | sample_4 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView vv5.2.2, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
NMR spectrometers:
- Bruker Avance 900 MHz
- Bruker Avance 800 MHz
- Bruker Avance 700 MHz
- Bruker Avance 600 MHz
- Bruker Avance 500 MHz
Related Database Links:
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts