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- PDB-2kok: Solution structure of an arsenate reductase (ArsC) related protei... -

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Basic information

Entry
Database: PDB / ID: 2kok
TitleSolution structure of an arsenate reductase (ArsC) related protein from Brucella melitensis. Seattle Structural Genomics Center for Infectious Disease target BrabA.00007.a.
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / arsenate reductase / brucellosis / zoonotic / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arsenate reductase / ArsC family protein
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis.
Authors: Buchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionSep 23, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arsenate reductase


Theoretical massNumber of molelcules
Total (without water)13,7781
Polymers13,7781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein arsenate reductase


Mass: 13777.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: ArsC, BruAb1_0395 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57EZ2, UniProt: Q2YMA4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D C(CO)NH
1913D H(CCO)NH
1102deuterium exchange
11113D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM BR7, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM BR7, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMBR7-11
100 mMsodium chloride-21
20 mMTRIS-31
1 mMDTT-41
1.0 mMBR7-52
100 mMsodium chloride-62
20 mMTRIS-72
1 mMDTT-82
Sample conditionsIonic strength: 0.12 / pH: 7.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTO NOESYASSIGN).
NMR constraintsNOE constraints total: 1054 / NOE intraresidue total count: 436 / NOE long range total count: 323 / NOE medium range total count: 282 / NOE sequential total count: 449 / Protein phi angle constraints total count: 94 / Protein psi angle constraints total count: 94
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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