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- PDB-1aiu: HUMAN THIOREDOXIN (D60N MUTANT, REDUCED FORM) -

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Basic information

Entry
Database: PDB / ID: 1aiu
TitleHUMAN THIOREDOXIN (D60N MUTANT, REDUCED FORM)
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / DIMER / THIOREDOXIN / D60N / REDOX-ACTIVE CENTER
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 Å
AuthorsAndersen, J.F. / Gasdaska, J.R. / Sanders, D.A.R. / Weichsel, A. / Powis, G. / Montfort, W.R.
CitationJournal: 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.
History
DepositionApr 25, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: 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 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 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)11,7491
Polymers11,7491
Non-polymers00
Water95553
1
A: THIOREDOXIN

A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)23,4992
Polymers23,4992
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)68.360, 26.760, 52.180
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOREDOXIN


Mass: 11749.493 Da / Num. of mol.: 1 / Mutation: D60N
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE CYSTEINES 32 AND 35 IN THE REDUCED FORM
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.02 Å3/Da / Density % sol: 38 %
Crystal growpH: 3.8 / Details: pH 3.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM1reservoirNaOAc
25 mMdithiothreitol1reservoir
350 %(v/v)MPD1reservoir
41
51
61
71

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 15, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 5545 / % possible obs: 85.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.038
Reflection
*PLUS
Num. measured all: 15528 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 75.3 % / Mean I/σ(I) obs: 8.4

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2→15 Å
RfactorNum. reflection% reflection
Rfree0.24 -10 %
Rwork0.179 --
obs0.179 9301 85.7 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 0 52 882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.673
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.525
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
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.24 -
Rwork0.27 526
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.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_deg24.905
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.525

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