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- PDB-3ctf: Crystal structure of oxidized GRX2 -

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Basic information

Entry
Database: PDB / ID: 3ctf
TitleCrystal structure of oxidized GRX2
ComponentsGlutaredoxin-2
KeywordsOXIDOREDUCTASE / OXIDIZED FORM / Electron transport / Mitochondrion / Redox-active center / Transit peptide / Transport
Function / homology
Function and homology information


glutathione peroxidase / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cellular response to oxidative stress / mitochondrion / nucleus ...glutathione peroxidase / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cellular response to oxidative stress / mitochondrion / nucleus / cytosol / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, J. / Teng, Y.B. / Zhou, C.Z.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Structural basis for the different activities of yeast Grx1 and Grx2.
Authors: Li, W.F. / Yu, J. / Ma, X.X. / Teng, Y.B. / Luo, M. / Tang, Y.J. / Zhou, C.Z.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin-2


Theoretical massNumber of molelcules
Total (without water)14,1501
Polymers14,1501
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.770, 48.770, 96.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-193-

HOH

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Components

#1: Protein Glutaredoxin-2 / / Thioltransferase / Glutathione-dependent oxidoreductase 2


Mass: 14150.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: GRX2, TTR, TTR1, YDR513W, D9719.17 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17695, arsenate reductase (glutathione/glutaredoxin)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.1M NAAC, 0.2M NH4AC, VAPOR DIFFUSION, HANGING DROP, pH 4.60, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
21.54181
ReflectionResolution: 2.1→28.05 Å / Num. obs: 12610 / % possible obs: 97.2 % / Redundancy: 3.56 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.3 / % possible all: 95.3

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Processing

Software
NameClassification
CNSrefinement
MAR345dtbdata collection
AUTOMARdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C1R

3c1r


Resolution: 2.1→28.05 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1136202.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 364 5.2 %RANDOM
Rwork0.222 ---
obs0.222 7063 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.49 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 0 105 936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
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
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 27 4 %
Rwork0.234 642 -
obs--94.9 %

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