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- PDB-2hsy: Solution structure of Thioredoxin 2 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2hsy
TitleSolution structure of Thioredoxin 2 from Saccharomyces cerevisiae
ComponentsThioredoxin II
KeywordsOXIDOREDUCTASE / thioredoxin
Function / homology
Function and homology information


membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species ...membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / glutathione metabolic process / cell redox homeostasis / protein transport / Golgi membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsAmorim, G.C. / Valente, A.P. / Almeida, F.C.L.
Citation
Journal: J.Biomol.Nmr / Year: 2007
Title: NMR solution structure of the reduced form of thioredoxin 2 from Saccharomyces cerevisiae
Authors: Amorim, G.C. / Pinheiro, A.S. / Netto, L.E.S. / Valente, A.P. / Almeida, F.C.L.
#1: Journal: J.Biomol.Nmr / Year: 2006
Title: (1)H, (13)C and (15)N Resonance Assignments for the Reduced Forms of Thioredoxin 1 and 2 from S. cerevisiae
Authors: Pinheiro, A.S. / Amorim, G.C. / Netto, L.E.S. / Valente, A.P. / Almeida, F.C.L.
History
DepositionJul 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Thioredoxin II


Theoretical massNumber of molelcules
Total (without water)11,2141
Polymers11,2141
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin II / TR-II / Thioredoxin 1


Mass: 11213.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22803

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N NOESY-HSQC
1213D 13C NOESY-HSQC
1312D NOESY
141HNCA-J

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Sample preparation

DetailsContents: 20mM phosphate buffer Na; 10mM DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1 / Details: cartesian simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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