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
MolProbity Validation Chart

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Title:
Solution NMR structure of integral membrane protein DsbB
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:

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).
PubMed: 18922471

Assembly members:

Assembly members:
Disulfide_bond_formation_protein_B, polymer, 183 residues, 20948.965 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Disulfide_bond_formation_protein_B: MLRFLNQASQGRGAWLLMAF TALALELTALWFQHVMLLKP CVLSIYERAALFGVLGAALI GAIAPKTPLRYVAMVIWLYS AFRGVQLTYEHTMLQLYPSP FATSDFMVRFPEWLPLDKWV PQVFVASGDCAERQWDFLGL EMPQWLLGIFIAYLIVAVLV VISQPFKAKKRDLFGRGHHH HHH

Data sets:
Data typeCount
13C chemical shifts499
15N chemical shifts170
1H chemical shifts170

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DsbB1

Entities:

Entity 1, DsbB 183 residues - 20948.965 Da.

residue 177-183 (-GHHHHHH) represents a non-native affinity tag and linker.

1   METLEUARGPHELEUASNGLNALASERGLN
2   GLYARGGLYALATRPLEULEUMETALAPHE
3   THRALALEUALALEUGLULEUTHRALALEU
4   TRPPHEGLNHISVALMETLEULEULYSPRO
5   CYSVALLEUSERILETYRGLUARGALAALA
6   LEUPHEGLYVALLEUGLYALAALALEUILE
7   GLYALAILEALAPROLYSTHRPROLEUARG
8   TYRVALALAMETVALILETRPLEUTYRSER
9   ALAPHEARGGLYVALGLNLEUTHRTYRGLU
10   HISTHRMETLEUGLNLEUTYRPROSERPRO
11   PHEALATHRSERASPPHEMETVALARGPHE
12   PROGLUTRPLEUPROLEUASPLYSTRPVAL
13   PROGLNVALPHEVALALASERGLYASPCYS
14   ALAGLUARGGLNTRPASPPHELEUGLYLEU
15   GLUMETPROGLNTRPLEULEUGLYILEPHE
16   ILEALATYRLEUILEVALALAVALLEUVAL
17   VALILESERGLNPROPHELYSALALYSLYS
18   ARGASPLEUPHEGLYARGGLYHISHISHIS
19   HISHISHIS

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:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCO based RDC experimentssample_1anisotropic polyacrylamid gelsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D 13C-13C NOESYsample_2isotropicsample_conditions_1
3D HMCM[CG]CBCAsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_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
AlphaFold P0A6M2 P0A6M3 Q0T5L6 Q31ZM6 Q32H31

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks