BMRB Entry 18493
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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/BMR18493
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Title: High resolution structure of DsbB C41S by joint calculation with solid-state NMR and X-ray data PubMed: 23416557
Deposition date: 2012-05-30 Original release date: 2013-02-27
Authors: Tang, Ming; Sperling, Lindsay; Schwieters, Charles; Nesbitt, Anna; Gennis, Robert; Rienstra, Chad
Citation: Tang, Ming; Nesbitt, Anna; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Gennis, Robert; Rienstra, Chad. "Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer." J. Mol. Biol. 425, 1670-1682 (2013).
Assembly members:
DsbB, polymer, 176 residues, 16663.053 Da.
entity_2, polymer, 239 residues, 24077.834 Da.
entity_3, polymer, 221 residues, 23024.885 Da.
entity_UQ1, non-polymer, 250.290 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):
DsbB: MLRFLNQASQGRGAWLLMAF
TALALELTALWFQHVMLLKP
SVLCIYERVALFGVLGAALI
GAIAPKTPLRYVAMVIWLYS
AFRGVQLTYEHTMLQLYPSP
FATCDFMVRFPEWLPLDKWV
PQVFVASGDCAERQWDFLGL
EMPQWLLGIFIAYLIVAVLV
VISQPFKAKKRDLFGR
entity_2: MDSQAQVLILLLLWVSGTCG
DIVMSQSPSSLAVSAGEKVT
MSCKSSQSLLNSRTRKNYLA
WYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLT
ISSVQAEDLAVYYCKQSYNL
YTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCF
LNNFYPKDINVKWKIDGSER
QNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCE
ATHKTSTSPIVKSFNRNEC
entity_3: EVQLVESGGGLVKPGGSLKL
SCAASGFAFSSYDMSWVRQT
PEKRLEWVAYISSGGGSTYY
PDTVKGRFTISRDNAKNTLY
LQMSSLKSEDTAMYYCARPD
YRSYAMDYWGQGTSVTVSSA
KTTAPSVYPLAPVCGDTTGS
SVTLGCLVKGYFPEPVTLTW
NSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSIT
CNVAHPASSTKVDKKIEPRG
P
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 552 |
| 15N chemical shifts | 125 |
| 1H chemical shifts | 67 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DsbB_1 | 1 |
| 2 | entity_2_1 | 2 |
| 3 | entity_3_1 | 3 |
| 4 | DsbB_2 | 1 |
| 5 | entity_2_2 | 2 |
| 6 | entity_3_2 | 3 |
| 7 | UBIQUINONE-1_1 | 4 |
| 8 | UBIQUINONE-1_2 | 4 |
Entities:
Entity 1, DsbB_1 176 residues - 16663.053 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 2, entity_2_1 239 residues - 24077.834 Da.
| 1 | MET | ASP | SER | GLN | ALA | GLN | VAL | LEU | ILE | LEU | ||||
| 2 | LEU | LEU | LEU | TRP | VAL | SER | GLY | THR | CYS | GLY | ||||
| 3 | ASP | ILE | VAL | MET | SER | GLN | SER | PRO | SER | SER | ||||
| 4 | LEU | ALA | VAL | SER | ALA | GLY | GLU | LYS | VAL | THR | ||||
| 5 | MET | SER | CYS | LYS | SER | SER | GLN | SER | LEU | LEU | ||||
| 6 | ASN | SER | ARG | THR | ARG | LYS | ASN | TYR | LEU | ALA | ||||
| 7 | TRP | TYR | GLN | GLN | LYS | PRO | GLY | GLN | SER | PRO | ||||
| 8 | LYS | LEU | LEU | ILE | TYR | TRP | ALA | SER | THR | ARG | ||||
| 9 | GLU | SER | GLY | VAL | PRO | ASP | ARG | PHE | THR | GLY | ||||
| 10 | SER | GLY | SER | GLY | THR | ASP | PHE | THR | LEU | THR | ||||
| 11 | ILE | SER | SER | VAL | GLN | ALA | GLU | ASP | LEU | ALA | ||||
| 12 | VAL | TYR | TYR | CYS | LYS | GLN | SER | TYR | ASN | LEU | ||||
| 13 | TYR | THR | PHE | GLY | GLY | GLY | THR | LYS | LEU | GLU | ||||
| 14 | ILE | LYS | ARG | ALA | ASP | ALA | ALA | PRO | THR | VAL | ||||
| 15 | SER | ILE | PHE | PRO | PRO | SER | SER | GLU | GLN | LEU | ||||
| 16 | THR | SER | GLY | GLY | ALA | SER | VAL | VAL | CYS | PHE | ||||
| 17 | LEU | ASN | ASN | PHE | TYR | PRO | LYS | ASP | ILE | ASN | ||||
| 18 | VAL | LYS | TRP | LYS | ILE | ASP | GLY | SER | GLU | ARG | ||||
| 19 | GLN | ASN | GLY | VAL | LEU | ASN | SER | TRP | THR | ASP | ||||
| 20 | GLN | ASP | SER | LYS | ASP | SER | THR | TYR | SER | MET | ||||
| 21 | SER | SER | THR | LEU | THR | LEU | THR | LYS | ASP | GLU | ||||
| 22 | TYR | GLU | ARG | HIS | ASN | SER | TYR | THR | CYS | GLU | ||||
| 23 | ALA | THR | HIS | LYS | THR | SER | THR | SER | PRO | ILE | ||||
| 24 | VAL | LYS | SER | PHE | ASN | ARG | ASN | GLU | CYS |
Entity 3, entity_3_1 221 residues - 23024.885 Da.
| 1 | GLU | VAL | GLN | LEU | VAL | GLU | SER | GLY | GLY | GLY | ||||
| 2 | LEU | VAL | LYS | PRO | GLY | GLY | SER | LEU | LYS | LEU | ||||
| 3 | SER | CYS | ALA | ALA | SER | GLY | PHE | ALA | PHE | SER | ||||
| 4 | SER | TYR | ASP | MET | SER | TRP | VAL | ARG | GLN | THR | ||||
| 5 | PRO | GLU | LYS | ARG | LEU | GLU | TRP | VAL | ALA | TYR | ||||
| 6 | ILE | SER | SER | GLY | GLY | GLY | SER | THR | TYR | TYR | ||||
| 7 | PRO | ASP | THR | VAL | LYS | GLY | ARG | PHE | THR | ILE | ||||
| 8 | SER | ARG | ASP | ASN | ALA | LYS | ASN | THR | LEU | TYR | ||||
| 9 | LEU | GLN | MET | SER | SER | LEU | LYS | SER | GLU | ASP | ||||
| 10 | THR | ALA | MET | TYR | TYR | CYS | ALA | ARG | PRO | ASP | ||||
| 11 | TYR | ARG | SER | TYR | ALA | MET | ASP | TYR | TRP | GLY | ||||
| 12 | GLN | GLY | THR | SER | VAL | THR | VAL | SER | SER | ALA | ||||
| 13 | LYS | THR | THR | ALA | PRO | SER | VAL | TYR | PRO | LEU | ||||
| 14 | ALA | PRO | VAL | CYS | GLY | ASP | THR | THR | GLY | SER | ||||
| 15 | SER | VAL | THR | LEU | GLY | CYS | LEU | VAL | LYS | GLY | ||||
| 16 | TYR | PHE | PRO | GLU | PRO | VAL | THR | LEU | THR | TRP | ||||
| 17 | ASN | SER | GLY | SER | LEU | SER | SER | GLY | VAL | HIS | ||||
| 18 | THR | PHE | PRO | ALA | VAL | LEU | GLN | SER | ASP | LEU | ||||
| 19 | TYR | THR | LEU | SER | SER | SER | VAL | THR | VAL | THR | ||||
| 20 | SER | SER | THR | TRP | PRO | SER | GLN | SER | ILE | THR | ||||
| 21 | CYS | ASN | VAL | ALA | HIS | PRO | ALA | SER | SER | THR | ||||
| 22 | LYS | VAL | ASP | LYS | LYS | ILE | GLU | PRO | ARG | GLY | ||||
| 23 | PRO |
Entity 4, UBIQUINONE-1_1 - C14 H18 O4 - 250.290 Da.
| 1 | UQ1 |
Samples:
sample_1: DsbB, [U-100% 13C; U-100% 15N], 7 mg; DDM 2 mg; E. coli lipids 7 mg
sample_2: DsbB, [2-13C-glycerol; U-15N], 5 mg; DDM 2 mg; E. coli lipids 7 mg
sample_3: DsbB, [1,3-13C-glycerol; U-15N], 4 mg; DDM 2 mg; E. coli lipids 7 mg
sample_conditions_1: 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 |
| 3D NCACX | sample_1 | solid | sample_conditions_1 |
| 3D NCOCX | sample_1 | 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:
| PDB | |
| BMRB | 15546 15966 18395 |
| DBJ | BAA36032 BAB35103 BAG76757 BAI24997 BAI30121 |
| EMBL | CAP75720 CAQ31687 CAQ98064 CAR02574 CAR12682 CAA75918 |
| GB | AAA23711 AAB25233 AAC74269 AAG56036 AAN42789 AAA53292 AAB47613 AAL04472 AEB66102 EDK98900 AAN06761 |
| PIR | H85696 G33932 PS0023 |
| REF | NP_309707 NP_415703 NP_707082 WP_000652474 WP_000943442 |
| SP | A1AAA8 P0A6M2 P0A6M3 P59343 Q0T5L6 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts