BMRB Entry 17710
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17710
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Title: Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data PubMed: 21938394
Deposition date: 2011-06-15 Original release date: 2011-10-12
Authors: Tang, Ming; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Nesbitt, Anna; Nieuwkoop, Andrew; Gennis, Robert; Rienstra, Chad
Citation: Tang, Ming; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Nesbitt, Anna; Nieuwkoop, Andrew; Gennis, Robert; Rienstra, Chad. "High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data." J. Biomol. NMR 51, 227-233 (2011).
Assembly members:
DsbA, polymer, 188 residues, 20993.951 Da.
DsbB, polymer, 176 residues, 15287.664 Da.
ZN, non-polymer, 65.409 Da.
UQ8, non-polymer, 727.109 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):
DsbA: AQYEDGKQYTTLEKPVAGAP
QVLEFFSFFCPHCYQFEEVL
HISDNVKKKLPEGVKMTKYH
VNFMGGDLGKDLTQAWAVAM
ALGVEDKVTVPLFEGVQKTQ
TIRSASDIRDVFINAGIKGE
EYDAAWNSFVVKSLVAQQEK
AAADVQLRGVPAMFVNGKYQ
LNPQGMDTSNMDVFVQQYAD
TVKYLSEK
DsbB: MLRFLNQASQGRGAWLLMAF
TALALELTALWFQHVMLLKP
SVLCIYERVALFGVLGAALI
GAIAPKTPLRYVAMVIWLYS
AFRGVQLTYEHTMLQLYPSP
FATCDFMVRFPEWLPLDKWV
PQVFVASGDCAERQWDFLGL
EMPQWLLGIFIAYLIVAVLV
VISQPFKAKKRDLFGR
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 1228 |
| 15N chemical shifts | 288 |
| 1H chemical shifts | 67 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DsbA | 1 |
| 2 | DsbB | 2 |
| 3 | ZINC ION | 3 |
| 4 | UBIQUINONE-1 | 4 |
Entities:
Entity 1, DsbA 188 residues - 20993.951 Da.
| 1 | ALA | GLN | TYR | GLU | ASP | GLY | LYS | GLN | TYR | THR | ||||
| 2 | THR | LEU | GLU | LYS | PRO | VAL | ALA | GLY | ALA | PRO | ||||
| 3 | GLN | VAL | LEU | GLU | PHE | PHE | SER | PHE | PHE | CYS | ||||
| 4 | PRO | HIS | CYS | TYR | GLN | PHE | GLU | GLU | VAL | LEU | ||||
| 5 | HIS | ILE | SER | ASP | ASN | VAL | LYS | LYS | LYS | LEU | ||||
| 6 | PRO | GLU | GLY | VAL | LYS | MET | THR | LYS | TYR | HIS | ||||
| 7 | VAL | ASN | PHE | MET | GLY | GLY | ASP | LEU | GLY | LYS | ||||
| 8 | ASP | LEU | THR | GLN | ALA | TRP | ALA | VAL | ALA | MET | ||||
| 9 | ALA | LEU | GLY | VAL | GLU | ASP | LYS | VAL | THR | VAL | ||||
| 10 | PRO | LEU | PHE | GLU | GLY | VAL | GLN | LYS | THR | GLN | ||||
| 11 | THR | ILE | ARG | SER | ALA | SER | ASP | ILE | ARG | ASP | ||||
| 12 | VAL | PHE | ILE | ASN | ALA | GLY | ILE | LYS | GLY | GLU | ||||
| 13 | GLU | TYR | ASP | ALA | ALA | TRP | ASN | SER | PHE | VAL | ||||
| 14 | VAL | LYS | SER | LEU | VAL | ALA | GLN | GLN | GLU | LYS | ||||
| 15 | ALA | ALA | ALA | ASP | VAL | GLN | LEU | ARG | GLY | VAL | ||||
| 16 | PRO | ALA | MET | PHE | VAL | ASN | GLY | LYS | TYR | GLN | ||||
| 17 | LEU | ASN | PRO | GLN | GLY | MET | ASP | THR | SER | ASN | ||||
| 18 | MET | ASP | VAL | PHE | VAL | GLN | GLN | TYR | ALA | ASP | ||||
| 19 | THR | VAL | LYS | TYR | LEU | SER | GLU | LYS |
Entity 2, DsbB 176 residues - 15287.664 Da.
| 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 | SER | VAL | LEU | CYS | ILE | TYR | GLU | ARG | VAL | 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 | CYS | 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 |
Entity 3, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Entity 4, UBIQUINONE-1 - C49 H74 O4 - 727.109 Da.
| 1 | UQ8 |
Samples:
sample_1: DsbA, [U-100% 13C; U-100% 15N], 15 mg; H2O 90%; D2O 10%
sample_2: DsbA, [2-13C-glycerol; U-15N], 10 mg; H2O 90%; D2O 10%
sample_3: DsbA, [1,3-13C-glycerol; U-15N], 10 mg; H2O 90%; D2O 10%
sample_4: DsbB, [U-100% 13C; U-100% 15N], 7 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%
sample_5: DsbB, [2-13C-glycerol; U-15N], 5 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%
sample_6: DsbB, [1,3-13C-glycerol; U-15N], 4 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%
sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 270 K
sample_conditions_2: pH: 7.8; pressure: 1 atm; temperature: 261 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D CC DARR | sample_1 | solid | sample_conditions_1 |
| 2D CC DARR | sample_2 | solid | sample_conditions_1 |
| 2D CC DARR | sample_3 | solid | sample_conditions_1 |
| 2D CC DARR | sample_4 | solid | sample_conditions_2 |
| 2D CC DARR | sample_5 | solid | sample_conditions_2 |
| 2D CC DARR | sample_6 | solid | sample_conditions_2 |
| 3D NCACX | sample_1 | solid | sample_conditions_1 |
| 3D NCACX | sample_2 | solid | sample_conditions_1 |
| 3D NCACX | sample_4 | solid | sample_conditions_2 |
| 3D NCOCX | sample_1 | solid | sample_conditions_1 |
| 3D NCOCX | sample_3 | solid | sample_conditions_1 |
| 3D NCOCX | sample_4 | solid | sample_conditions_2 |
| 3D CAN(CO)CX | sample_1 | solid | sample_conditions_1 |
| 3D CAN(CO)CX | sample_4 | solid | sample_conditions_2 |
| 3D CON(CA)CX | sample_4 | solid | sample_conditions_2 |
| 4D CANCOCX | sample_1 | solid | sample_conditions_1 |
| 2D NC TEDOR | sample_3 | solid | sample_conditions_1 |
Software:
SPARKY, Goddard - chemical shift assignment
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
TALOS+, Shen, Cornilescu, Delaglio and Bax - data analysis
VNMRJ, Varian - collection
NMR spectrometers:
- Varian INOVA 750 MHz
- Varian VXRS 500 MHz
Related Database Links:
| BMRB | 16327 18396 18543 18544 15546 15966 18395 18493 18544 |
| PDB | |
| DBJ | BAB38206 BAE77448 BAG79665 BAI27892 BAI33015 BAA36032 BAB35103 BAG76757 BAI24997 BAI30121 |
| EMBL | CAA44868 CAA56736 CAA90910 CAP78318 CAQ34212 CAP75720 CAQ31687 CAQ98064 CAR02574 CAR12682 |
| GB | AAA23715 AAB02995 AAC43519 AAC43520 AAC43521 AAA23711 AAB25233 AAC74269 AAG56036 AAN42789 |
| REF | NP_312810 NP_418297 NP_709659 WP_000725331 WP_000725332 NP_287424 NP_309707 NP_415703 NP_707082 NP_753538 |
| SP | P0A4L5 P0A4L6 P0AEG4 P0AEG5 P52235 A1AAA8 P0A6M2 P0A6M3 P59343 Q0T5L6 |
| PIR | H85696 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts