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- PDB-2ipa: solution structure of Trx-ArsC complex -

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Basic information

Entry
Database: PDB / ID: 2ipa
Titlesolution structure of Trx-ArsC complex
Components
  • Protein arsC
  • Thioredoxin
KeywordsElectron transport/Oxidoreductase / solution structure / complex / Electron transport-Oxidoreductase COMPLEX
Function / homology
Function and homology information


arsenate reductase (thioredoxin) / arsenate reductase (thioredoxin) activity / response to arsenic-containing substance / protein-disulfide reductase activity / cell redox homeostasis / protein tyrosine phosphatase activity / cytosol / cytoplasm
Similarity search - Function
Arsenate reductase ArsC / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Response regulator ...Arsenate reductase ArsC / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Response regulator / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Arsenate reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsJin, C. / Hu, Y. / Li, Y. / Zhang, X.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Conformational fluctuations coupled to the thiol-disulfide transfer between thioredoxin and arsenate reductase in Bacillus subtilis.
Authors: Li, Y. / Hu, Y. / Zhang, X. / Xu, H. / Lescop, E. / Xia, B. / Jin, C.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Protein arsC


Theoretical massNumber of molelcules
Total (without water)26,9382
Polymers26,9382
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Thioredoxin / / TRX


Mass: 11388.071 Da / Num. of mol.: 1 / Mutation: C32S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14949
#2: Protein Protein arsC / Arsenate reductase / Arsenical pump modifier / Low molecular weight protein-tyrosine-phosphatase


Mass: 15550.283 Da / Num. of mol.: 1 / Mutation: C10SC15AC82S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P45947, EC: 1.20.4.-, protein-tyrosine-phosphatase

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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
1323D 13C-separated NOESY
1423D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Trx(U-15N, 13C)-ArsC; 20mM Tris buffer; 20mM Na2SO4; 40mM KCl 90% H2O, 10% D2O90% H2O/10% D2O
22mM Trx-ArsC(U-15N, 13C); 20mM Tris buffer; 20mM Na2SO4; 40mM KCl 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 80mM / pH: 6.85 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.1Frank Delaglioprocessing
NMRView5Bruce Johnsondata analysis
CNS1.1Brunger, A.T.structure solution
Amber7David Caserefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

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