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- PDB-2ijy: NMR structure ensemble for the reduced DsbA disulphide oxidoreduc... -

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Basic information

Entry
Database: PDB / ID: 2ijy
TitleNMR structure ensemble for the reduced DsbA disulphide oxidoreductase from Vibrio Cholerae
ComponentsThiol:disulfide interchange protein dsbA
KeywordsOXIDOREDUCTASE / thioredoxin domain / helical domain insert
Function / homology
Function and homology information


periplasmic space / oxidoreductase activity
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHorne, J.H. / Velkov, T. / Scanlon, M.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Probing the Flexibility of the DsbA Oxidoreductase from Vibrio cholerae-a (15)N - (1)H Heteronuclear NMR Relaxation Analysis of Oxidized and Reduced Forms of DsbA.
Authors: Horne, J. / d'Auvergne, E.J. / Coles, M. / Velkov, T. / Chin, Y. / Charman, W.N. / Prankerd, R. / Gooley, P.R. / Scanlon, M.J.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbA


Theoretical massNumber of molelcules
Total (without water)20,4951
Polymers20,4951
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)22 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thiol:disulfide interchange protein dsbA


Mass: 20495.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: dsbA, tpcG / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P32557, protein-disulfide reductase (glutathione)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: Structure determined using triple resonance methods. Stereospecific assignments of valine and leucine methyls were achieved using a 10% 13C-labeled sample of DsbA

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM DsbA U-15N,13C, 10 mM HEPES, 50 mM sodium chloride, ph 6.8, 90% H2O, 10% D2O90% H2O/10% D2O
2400 uM DsbA 10%-13C, 10 mM HEPES, 50 mM sodium chloride, ph 6.8, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 320 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian AVANCEVarianAVANCE6002

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
VNMRcollection
NMRPipeprocessing
Sparkydata analysis
CYANA2.1structure solution
X-PLORrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 898 long range NOE restraints, 850 medium range NOE restraints, 95 ambiguous NOE restraints, 95 hydrogen bond distance restraints, 238 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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