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- PDB-2jsy: Solution structure of Tpx in the oxidized state -

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Basic information

Entry
Database: PDB / ID: 2jsy
TitleSolution structure of Tpx in the oxidized state
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE / solution structure / Antioxidant / Peroxidase
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsJin, C. / Lu, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Reversible conformational switch revealed by the redox structures of Bacillus subtilis thiol peroxidase
Authors: Lu, J. / Yang, F. / Li, Y. / Zhang, X. / Xia, B. / Jin, C.
History
DepositionJul 17, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)18,2361
Polymers18,2361
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)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Probable thiol peroxidase / Superoxide-inducible protein 8 / SOI8


Mass: 18235.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tpx, ytgI / Production host: Escherichia coli (E. coli)
References: UniProt: P80864, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] Tpx, 20 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTpx[U-13C; U-15N]1
20 mMsodium phosphate1
Sample conditionsIonic strength: 20 / pH: 7.0 / Pressure units: atm / Temperature: 303 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
XwinNMR3.5Bruker Biospincollection
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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