BMRB Entry 15966
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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/BMR15966
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Title: Solution NMR structure of integral membrane protein DsbB PubMed: 18922471
Deposition date: 2008-09-25 Original release date: 2008-12-12
Authors: Zhou, Yunpeng; Cierpicki, Tomasz; Flores Jimenez, Ricardo; Lukasik, Stephen; Ellena, Jeffrey; Cafiso, David; Kadukura, Hiroshi; Beckwith, Jon; Bushweller, John
Citation: Zhou, Yunpeng; Cierpicki, Tomasz; Flores Jimenez, Ricardo; Lukasik, Stephen; Ellena, Jeffrey; Cafiso, David; Kadukura, Hiroshi; Beckwith, Jon; Bushweller, John. "NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation." Mol. Cell 31, 896-908 (2008).
Assembly members:
Disulfide_bond_formation_protein_B, polymer, 183 residues, 20948.965 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Disulfide_bond_formation_protein_B: MLRFLNQASQGRGAWLLMAF
TALALELTALWFQHVMLLKP
CVLSIYERAALFGVLGAALI
GAIAPKTPLRYVAMVIWLYS
AFRGVQLTYEHTMLQLYPSP
FATSDFMVRFPEWLPLDKWV
PQVFVASGDCAERQWDFLGL
EMPQWLLGIFIAYLIVAVLV
VISQPFKAKKRDLFGRGHHH
HHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 499 |
| 15N chemical shifts | 170 |
| 1H chemical shifts | 170 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DsbB | 1 |
Entities:
Entity 1, DsbB 183 residues - 20948.965 Da.
residue 177-183 (-GHHHHHH) represents a non-native affinity tag and linker.
| 1 | MET | LEU | ARG | PHE | LEU | ASN | GLN | ALA | SER | GLN | ||||
| 2 | GLY | ARG | GLY | ALA | TRP | LEU | LEU | MET | ALA | PHE | ||||
| 3 | THR | ALA | LEU | ALA | LEU | GLU | LEU | THR | ALA | LEU | ||||
| 4 | TRP | PHE | GLN | HIS | VAL | MET | LEU | LEU | LYS | PRO | ||||
| 5 | CYS | VAL | LEU | SER | ILE | TYR | GLU | ARG | ALA | ALA | ||||
| 6 | LEU | PHE | GLY | VAL | LEU | GLY | ALA | ALA | LEU | ILE | ||||
| 7 | GLY | ALA | ILE | ALA | PRO | LYS | THR | PRO | LEU | ARG | ||||
| 8 | TYR | VAL | ALA | MET | VAL | ILE | TRP | LEU | TYR | SER | ||||
| 9 | ALA | PHE | ARG | GLY | VAL | GLN | LEU | THR | TYR | GLU | ||||
| 10 | HIS | THR | MET | LEU | GLN | LEU | TYR | PRO | SER | PRO | ||||
| 11 | PHE | ALA | THR | SER | ASP | PHE | MET | VAL | ARG | PHE | ||||
| 12 | PRO | GLU | TRP | LEU | PRO | LEU | ASP | LYS | TRP | VAL | ||||
| 13 | PRO | GLN | VAL | PHE | VAL | ALA | SER | GLY | ASP | CYS | ||||
| 14 | ALA | GLU | ARG | GLN | TRP | ASP | PHE | LEU | GLY | LEU | ||||
| 15 | GLU | MET | PRO | GLN | TRP | LEU | LEU | GLY | ILE | PHE | ||||
| 16 | ILE | ALA | TYR | LEU | ILE | VAL | ALA | VAL | LEU | VAL | ||||
| 17 | VAL | ILE | SER | GLN | PRO | PHE | LYS | ALA | LYS | LYS | ||||
| 18 | ARG | ASP | LEU | PHE | GLY | ARG | GLY | HIS | HIS | HIS | ||||
| 19 | HIS | HIS | HIS |
Samples:
sample_1: DsbB[CSSC], [U-13C; U-15N; U-2H], 1.2 mM; DPC, [U-2H], 100 mM; sodium phosphate 25 mM; potassium chloride 50 mM
sample_2: DsbB[CSSC], I,L,V methyl protonated, [U-13C; U-15N; U-2H], 1.5 mM; DPC, [U-2H], 100 mM; sodium phosphate 25 mM; potassium chloride 50 mM
sample_3: DsbB[CSSC] single Cys mutants, [U-15N; U-2H], 0.5 – 1.0 mM; DPC 100 mM; sodium phosphate 25 mM; potassium chloride 50 mM
sample_conditions_1: ionic strength: 0.1 M; pH: 6.2; pressure: 1 atm; temperature: 313 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO based RDC experiments | sample_1 | anisotropic polyacrylamid gel | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D HMCM[CG]CBCA | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
Software:
VNMR, Varian - collection
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment, data analysis
Molmol, Koradi, Billeter and Wuthrich - data analysis
NMR spectrometers:
- Varian INOVA 600 MHz
Related Database Links:
| BMRB | 18395 18493 |
| PDB | |
| DBJ | BAA36032 BAB35103 BAI24997 BAI30121 BAI35441 |
| EMBL | CAQ31687 CAQ98064 CAR12682 CAR18016 CAU97139 |
| GB | AAA23711 AAB25233 AAC74269 AAG56036 AAN42789 |
| PIR | H85696 |
| REF | NP_309707 NP_415703 NP_707082 WP_000652474 WP_000943442 |
| SP | P0A6M2 P0A6M3 Q0T5L6 Q31ZM6 Q32H31 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts