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- PDB-3c1s: Crystal structure of GRX1 in glutathionylated form -

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Basic information

Entry
Database: PDB / ID: 3c1s
TitleCrystal structure of GRX1 in glutathionylated form
ComponentsGlutaredoxin-1
KeywordsOXIDOREDUCTASE / GLUTATHIONYLATED FORM
Function / homology
Function and homology information


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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYu, J. / Zhou, C.Z.
CitationJournal: Proteins / Year: 2008
Title: Glutathionylation-triggered conformational changes of glutaredoxin Grx1 from the yeast Saccharomyces cerevisiae.
Authors: Yu, J. / Zhang, N.N. / Yin, P.D. / Cui, P.X. / Zhou, C.Z.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)13,7192
Polymers13,4111
Non-polymers3071
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.195, 77.571, 100.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 13411.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Gene: GRX1 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P25373, arsenate reductase (glutathione/glutaredoxin)
#2: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 20% PEG 4000, 0.1M SODIUM ACETATE, 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / 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 wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.74 Å / Num. obs: 4547 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2.79 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.0918 / Net I/σ(I): 4.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.82 % / Rmerge(I) obs: 0.1787 / Mean I/σ(I) obs: 2.9 / Num. unique all: 418 / % possible all: 99.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
MAR345dtbdata collection
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C1R

3c1r


Resolution: 2.5→29.74 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 883820.03 / 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
Rfree0.253 228 5.1 %RANDOM
Rwork0.221 ---
obs0.221 4501 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.92 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 20 73 940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.6
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: 2.5→2.59 Å / Rfactor Rfree error: 0.075 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.309 228 3.9 %
Rwork0.251 418 -
obs-4501 97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GSH_PARA.PARAMGSH_TOPO.TOP

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