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- PDB-3d5j: Structure of yeast Grx2-C30S mutant with glutathionyl mixed disulfide -

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Basic information

Entry
Database: PDB / ID: 3d5j
TitleStructure of yeast Grx2-C30S mutant with glutathionyl mixed disulfide
ComponentsGlutaredoxin-2, mitochondrial
KeywordsOXIDOREDUCTASE / yeast Grx2-C30S / 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
GLUTATHIONE / Glutaredoxin-2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsDiscola, K.F. / de Oliveira, M.A. / Barcena, J.A. / Porras, P. / Padilla, C.A. / Guimaraes, B.G. / Netto, L.E.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae.
Authors: Discola, K.F. / de Oliveira, M.A. / Rosa Cussiol, J.R. / Monteiro, G. / Barcena, J.A. / Porras, P. / Padilla, C.A. / Guimaraes, B.G. / Netto, L.E.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin-2, mitochondrial
B: Glutaredoxin-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2534
Polymers24,6382
Non-polymers6152
Water2,324129
1
A: Glutaredoxin-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6262
Polymers12,3191
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaredoxin-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6262
Polymers12,3191
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.008, 45.205, 105.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12319.102 Da / Num. of mol.: 2 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GRX2, TTR, TTR1, YDR513W, D9719.17 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17695
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.782967 Å3/Da / Density % sol: 31.013851 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.91→37.01 Å / Num. obs: 14326 / % possible obs: 99.7 % / Redundancy: 8.6 % / Biso Wilson estimate: 14.753 Å2 / Rsym value: 0.389 / Net I/σ(I): 23.6
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.07 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→34.9 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.416 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 720 5 %RANDOM
Rwork0.198 ---
obs0.201 14290 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 40 129 1818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221714
X-RAY DIFFRACTIONr_angle_refined_deg1.4342.0042319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3515219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18327.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40515303
X-RAY DIFFRACTIONr_chiral_restr0.1020.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021252
X-RAY DIFFRACTIONr_nbd_refined0.2350.21057
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.228
X-RAY DIFFRACTIONr_mcbond_it0.6611.51112
X-RAY DIFFRACTIONr_mcangle_it1.17321755
X-RAY DIFFRACTIONr_scbond_it1.9223649
X-RAY DIFFRACTIONr_scangle_it3.1244.5563
LS refinement shellResolution: 1.912→1.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 61 -
Rwork0.242 965 -
all-1026 -
obs--98.94 %

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