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- PDB-1eru: HUMAN THIOREDOXIN (OXIDIZED FORM) -

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Basic information

Entry
Database: PDB / ID: 1eru
TitleHUMAN THIOREDOXIN (OXIDIZED FORM)
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWeichsel, A. / Gasdaska, J.R. / Powis, G. / Montfort, W.R.
CitationJournal: Structure / Year: 1996
Title: Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer.
Authors: Weichsel, A. / Gasdaska, J.R. / Powis, G. / Montfort, W.R.
History
DepositionFeb 7, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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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)11,7501
Polymers11,7501
Non-polymers00
Water64936
1
A: THIOREDOXIN

A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)23,5012
Polymers23,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)67.830, 26.350, 51.790
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOREDOXIN


Mass: 11750.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE CYSTEINES 32 AND 35 IN THE OXIDIZED FORM
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 38 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 3.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium acetate1drop
225 %(v/v)MPD1drop
35 mMDTT1drop
450 %MPD1reservoir

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Data collection

DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 22, 1995
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 4440 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Num. measured all: 8894 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
MADNESdata collection
PROCORdata collection
FBSCALEdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
PROCORdata reduction
FBSCALEdata reduction
X-PLORphasing
RefinementResolution: 2.1→15 Å / σ(F): 0
RfactorNum. reflection
Rfree0.33 -
Rwork0.22 -
obs0.22 4440
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 36 857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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