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- PDB-1fo5: SOLUTION STRUCTURE OF REDUCED MJ0307 -

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Basic information

Entry
Database: PDB / ID: 1fo5
TitleSOLUTION STRUCTURE OF REDUCED MJ0307
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / disulfide oxidoreductase / thioredoxin fold / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity / cytoplasm
Similarity search - Function
Thioredoxins/glutaredoxin / Thioredoxin domain / Glutaredoxin active site / Glutaredoxin active site. / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin ...Thioredoxins/glutaredoxin / Thioredoxin domain / Glutaredoxin active site / Glutaredoxin active site. / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / torsion angle dynamics (DYANA) restrained energy minimization (OPAL)
AuthorsCave, J.W. / Cho, H.S. / Batchelder, A.M. / Kim, R. / Yokota, H. / Wemmer, D.E. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Protein Sci. / Year: 2001
Title: Solution nuclear magnetic resonance structure of a protein disulfide oxidoreductase from Methanococcus jannaschii.
Authors: Cave, J.W. / Cho, H.S. / Batchelder, A.M. / Yokota, H. / Kim, R. / Wemmer, D.E.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)9,4141
Polymers9,4141
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 / 60target function
RepresentativeModel #1lowest energy

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Components

#1: Protein THIOREDOXIN / MJ0307 PROTEIN DISULFIDE OXIDOREDUCTASE


Mass: 9414.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q57755

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HMQC-J
1232D NOESY
1313D 15N-separated NOESY
2423D 13C-separated NOESY
2524D 13C-separated NOESY
NMR detailsText: The structure was determined using 2D homonuclear techniques and triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Mj0307 U-15N; 35mM Sodium Phosphate pH 6.3, 5 mM DTT, 0.02% Sodium Azide90% H2O/10% D2O
21.5mM Mj0307 U-(15N,13C); 35mM Sodium Phosphate pH 6.3, 5 mM DTT, 0.02% Sodium Azide100% D2O
31.5mM Mj0307; 35mM Sodium Phosphate pH 6.3, 5 mM DTT, 0.02% Sodium Azide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
135mM sodium phosphate 6.3 ambient 308 K
235mM sodium phosphate 6.3 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR910901Brukercollection
XwinNMR2Brukercollection
Felix98MSI Biosymprocessing
DYANA1.5Guntert et al.structure solution
OPAL2.6Luginbuhl et al.refinement
RefinementMethod: torsion angle dynamics (DYANA) restrained energy minimization (OPAL)
Software ordinal: 1
Details: 505 upper limit distance constraints 52 backbone phi torsion angle constraints 30 hydrogen bond constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 60 / Conformers submitted total number: 20

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