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- PDB-2leg: Membrane protein complex DsbB-DsbA structure by joint calculation... -

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Basic information

Entry
Database: PDB / ID: 2leg
TitleMembrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data
Components
  • Disulfide bond formation protein B
  • Thiol:disulfide interchange protein DsbA
KeywordsMEMBRANE PROTEIN / OXIDOREDUCTASE / Disulfide bond / redox-active center / cell inner membrane / cell membrane / chaperone / electron transport / membrane / transmembrane / transport
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / ubiquinone binding / cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / protein folding / outer membrane-bounded periplasmic space / response to heat / electron transfer activity / plasma membrane
Similarity search - Function
Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site ...Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UBIQUINONE-1 / Disulfide bond formation protein B / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLID-STATE NMR / simulated annealing
Model detailsclosest to the average, model 8
AuthorsTang, M. / Sperling, L.J. / Berthold, D.A. / Schwieters, C.D. / Nesbitt, A.E. / Nieuwkoop, A.J. / Gennis, R.B. / Rienstra, C.M.
CitationJournal: J.Biomol.Nmr / Year: 2011
Title: High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
Authors: Tang, M. / Sperling, L.J. / Berthold, D.A. / Schwieters, C.D. / Nesbitt, A.E. / Nieuwkoop, A.J. / Gennis, R.B. / Rienstra, C.M.
History
DepositionJun 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
B: Disulfide bond formation protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5464
Polymers41,2302
Non-polymers3162
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21122.959 Da / Num. of mol.: 1 / Mutation: C33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG4
#2: Protein Disulfide bond formation protein B / / Disulfide oxidoreductase


Mass: 20106.982 Da / Num. of mol.: 1 / Mutation: C8A, C49V, C130S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbB, roxB, ycgA, b1185, JW5182 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6M2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D CC DARR
1222D CC DARR
1332D CC DARR
2442D CC DARR
2552D CC DARR
2662D CC DARR
1713D NCACX
1823D NCACX
2943D NCACX
11013D NCOCX
11133D NCOCX
21243D NCOCX
11313D CAN(CO)CX
21443D CAN(CO)CX
21543D CON(CA)CX
11614D CANCOCX
11732D NC TEDOR
NMR detailsText: Chemical shifts assignments and CC correlations provide dihedral angle and distance restraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
115 mg [U-100% 13C; U-100% 15N] DsbA, 90% H2O/10% D2O90% H2O/10% D2O
210 mg [2-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O90% H2O/10% D2O
310 mg [1,3-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O90% H2O/10% D2O
47 mg [U-100% 13C; U-100% 15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
55 mg [2-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
64 mg [1,3-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLDsbA-1[U-100% 13C; U-100% 15N]1
10 mg/mLDsbA-2[2-13C-glycerol; U-15N]2
10 mg/mLDsbA-3[1,3-13C-glycerol; U-15N]3
7 mg/mLDsbB-4[U-100% 13C; U-100% 15N]4
2 mg/mLDDM-54
7 mg/mLE. coli lipids-64
5 mg/mLDsbB-7[2-13C-glycerol; U-15N]5
2 mg/mLDDM-85
7 mg/mLE. coli lipids-95
4 mg/mLDsbB-10[1,3-13C-glycerol; U-15N]6
2 mg/mLDDM-116
7 mg/mLE. coli lipids-126
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 ambient 270 K
27.8 ambient 261 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian VXRSVarianVXRS5002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOS+Shen, Cornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Joint calculation of DsbB-DsbA complex with solid-state NMR restraints and X-ray reflections from PDB entry 2HI7.
NMR constraintsNOE constraints total: 811
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.51 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.52 Å
NMR ensemble rmsDistance rms dev: 0.121 Å / Distance rms dev error: 0.003 Å

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