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- PDB-2k73: Solution NMR structure of integral membrane protein DsbB -

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Basic information

Entry
Database: PDB / ID: 2k73
TitleSolution NMR structure of integral membrane protein DsbB
ComponentsDisulfide bond formation protein B
KeywordsMEMBRANE PROTEIN / OXIDOREDUCTASE / disulfide bond / redox enzyme / DsbB / Chaperone / Electron transport / Inner membrane / Redox-active center / 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 / protein-disulfide reductase activity / protein folding / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Disulfide bond formation protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, Y. / Cierpicki, T. / Flores Jimenez, R.H. / Lukasik, S.M. / Ellena, J.F. / Cafiso, D.S. / Kadokura, H. / Beckwith, J. / Bushweller, J.H.
CitationJournal: Mol.Cell / Year: 2008
Title: NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation.
Authors: Zhou, Y. / Cierpicki, T. / Jimenez, R.H. / Lukasik, S.M. / Ellena, J.F. / Cafiso, D.S. / Kadokura, H. / Beckwith, J. / Bushweller, J.H.
History
DepositionAug 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)20,9491
Polymers20,9491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 117structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Disulfide bond formation protein B / / Disulfide oxidoreductase


Mass: 20948.797 Da / Num. of mol.: 1 / Mutation: C8A, C44S, C49A, C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbB, roxB, ycgA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta(DE3) / References: UniProt: P0A6M2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CA)CO
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1612D 1H-15N HSQC
1713D HNCO based RDC experiments
1823D 1H-15N NOESY
1923D 1H-13C NOESY
11022D 1H-13C HSQC
11123D 13C-13C NOESY
11223D HMCM[CG]CBCA
11332D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-13C; U-15N; U-2H] DsbB[CSSC], 100 mM [U-2H] DPC, 25 mM sodium phosphate, 50 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM I,L,V methyl protonated, [U-13C; U-15N; U-2H] DsbB[CSSC], 100 mM [U-2H] DPC, 25 mM sodium phosphate, 50 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
30.75 mM [U-15N; U-2H] DsbB[CSSC] single Cys mutants, 100 mM DPC, 25 mM sodium phosphate, 50 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMDsbB[CSSC][U-13C; U-15N; U-2H]1
100 mMDPC[U-2H]1
25 mMsodium phosphate1
50 mMpotassium chloride1
1.5 mMDsbB[CSSC]I,L,V methyl protonated, [U-13C; U-15N; U-2H]2
100 mMDPC[U-2H]2
25 mMsodium phosphate2
50 mMpotassium chloride2
0.75 mMDsbB[CSSC] single Cys mutants[U-15N; U-2H]3
100 mMDPC3
25 mMsodium phosphate3
50 mMpotassium chloride3
Sample conditionsIonic strength: 0.1 / pH: 6.2 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 501 / NOE intraresidue total count: 41 / NOE long range total count: 39 / NOE medium range total count: 216 / NOE sequential total count: 191 / Hydrogen bond constraints total count: 97 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 144 / Protein psi angle constraints total count: 151
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 117 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.0099 Å / Distance rms dev error: 0.0008 Å

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