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- PDB-1auc: HUMAN THIOREDOXIN (OXIDIZED WITH DIAMIDE) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1auc
TitleHUMAN THIOREDOXIN (OXIDIZED WITH DIAMIDE)
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / DIMER / THIOREDOXIN / ELECTRON TRANSPORT
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 / cytosol / cytoplasm
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
AuthorsAnderson, J.F. / Sanders, D.A.R. / Gasdaska, J. / Weichsel, A. / Powis, G. / Montfort, W.R.
Citation
Journal: Biochemistry / Year: 1997
Title: Human thioredoxin homodimers: regulation by pH, role of aspartate 60, and crystal structure of the aspartate 60 --> asparagine mutant.
Authors: Andersen, J.F. / Sanders, D.A. / Gasdaska, J.R. / Weichsel, A. / Powis, G. / Montfort, W.R.
#1: Journal: 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
DepositionAug 22, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: 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
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,7501
Polymers11,7501
Non-polymers00
Water77543
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)67.750, 26.290, 51.620
Angle α, β, γ (deg.)90.00, 95.14, 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10599
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 38 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
27.25 mMdiamide1drop
35 mM1dropNaOAc
42.5 mMDTT1drop
59 %PEG40001drop
618 %PEG40001reservoir
7200 mM1reservoirNaOAc

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→26 Å / Num. obs: 5391 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rsym value: 0.027 / Net I/σ(I): 18.8
Reflection
*PLUS
Num. measured all: 8553 / Rmerge(I) obs: 0.027
Reflection shell
*PLUS
% possible obs: 94.4 % / Mean I/σ(I) obs: 7.9

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata reduction
FBSCALEdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.1→26 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.27 -10 %
Rwork0.19 --
obs0.19 5376 98 %
Displacement parametersBiso mean: 27 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 0 43 873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67

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