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- PDB-1erw: HUMAN THIOREDOXIN DOUBLE MUTANT WITH CYS 32 REPLACED BY SER AND C... -

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Basic information

Entry
Database: PDB / ID: 1erw
TitleHUMAN THIOREDOXIN DOUBLE MUTANT WITH CYS 32 REPLACED BY SER AND CYS 35 REPLACED BY SER
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / DIMER / THIOREDOXIN
Function / homology
Function and homology information


positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / cellular detoxification of hydrogen peroxide / 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 / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes ...positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / cellular detoxification of hydrogen peroxide / 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 / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / protein-disulfide reductase activity / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / 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: 1.8 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 1.0Oct 14, 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
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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)11,7181
Polymers11,7181
Non-polymers00
Water88349
1
A: THIOREDOXIN

A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)23,4372
Polymers23,4372
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)67.770, 26.380, 51.640
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOREDOXIN


Mass: 11718.349 Da / Num. of mol.: 1 / Mutation: C32S, C35S
Source method: isolated from a genetically manipulated source
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.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 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 mMdithiothreitol1drop
410 mMsodium acetate1reservoir
550 %(v/v)MPD1reservoir
65 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 7917 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. measured all: 23947
Reflection shell
*PLUS
% possible obs: 77 % / Mean I/σ(I) obs: 7.9

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Processing

Software
NameVersionClassification
MADNESdata collection
PROCORdata collection
FBSCALEdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata reduction
FBSCALEdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 -10 %
Rwork0.21 --
obs0.21 7877 91 %
Displacement parametersBiso mean: 18 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 49 870
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.14
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14

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