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- PDB-2jac: Glutaredoxin Grx1p C30S mutant from yeast -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2jac
TitleGlutaredoxin Grx1p C30S mutant from yeast
ComponentsGLUTAREDOXIN-1GLRX
KeywordsELECTRON TRANSPORT / REDOX-ACTIVE CENTER / OXIDOREDUCTASE / GLUTATHIONE / GLUTAREDOXIN
Function / homology
Function and homology information


protein glutathionylation / glutathione peroxidase / glutathione disulfide oxidoreductase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / cellular response to oxidative stress / nucleus / cytoplasm
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin-1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHakansson, K.O. / Winther, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of Glutaredoxin Grx1P C30S Mutant from Yeast.
Authors: Hakansson, K.O. / Winther, J.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallisation of Mutant Forms of Glutaredoxin Grx1P from Yeast
Authors: Hakansson, K.O. / Ostergaard, H. / Winther, J.R.
History
DepositionNov 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Dec 7, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.3Oct 22, 2014Group: Database references
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAREDOXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6852
Polymers12,3781
Non-polymers3071
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.023, 78.461, 100.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-3007-

HOH

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Components

#1: Protein GLUTAREDOXIN-1 / GLRX / GLUTAREDOXIN / GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 1


Mass: 12378.087 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25373
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 30 TO SER

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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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.75 / Details: 50MM CITRATE PH 4.75 10-22.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.115
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. obs: 8364 / % possible obs: 97.5 % / Observed criterion σ(I): -10 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 84.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CCP4phasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -5 %RANDOM
Rwork0.208 ---
obs0.208 8343 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 20 65 940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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