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- PDB-2b5x: Solution Structure of a Thioredoxin-like Protein in the Reduced Form -

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Basic information

Entry
Database: PDB / ID: 2b5x
TitleSolution Structure of a Thioredoxin-like Protein in the Reduced Form
ComponentsYkuV protein
KeywordsOXIDOREDUCTASE / Thioredoxin-like
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors / antioxidant activity / oxidoreductase activity / cytoplasm
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Thiol-disulfide oxidoreductase YkuV
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsZhang, X. / Xia, B. / Jin, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The bacillus subtilis YKUV is a thiol-disulfide oxidoreductase revealed by its redox structures and activity
Authors: Zhang, X. / Hu, Y. / Guo, X. / Lescop, E. / Li, Y. / Xia, B. / Jin, C.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: 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
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: YkuV protein


Theoretical massNumber of molelcules
Total (without water)17,0401
Polymers17,0401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein YkuV protein / trxy


Mass: 17040.279 Da / Num. of mol.: 1 / Fragment: residues 1-148
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: GenBank: 2632243, UniProt: O31699*PLUS

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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: ensembled structures plus mean structure

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Sample preparation

DetailsContents: 1mM Trxy U-15N, 13C; 50mM sodium phosphate, 100mM sodium chloride; 90% H2O 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 100mM sodium chloride
pH: 7.4 / Pressure: ambient / Temperature: 298.4 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
NMRPipe2.1F.Delaglio, S.Grzesiek, G.Vuister, G.Zhu, J.Pfeifer, A.Baxprocessing
SANEB.M.Duggan, G.B.Legge, H.J.Dyson, P.E.Wrightdata analysis
CYANA1.0.6P.Guntert, C.Mumenthaler, K.Wuthrichstructure solution
Amber7D.Caserefinement
NMRView5B.Johnsondata analysis
XwinNMR3.5Brukercollection
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: 50 / Conformers submitted total number: 11

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