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- PDB-6mws: crystal structure of the reduced Grx1 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6mws
Titlecrystal structure of the reduced Grx1 from Saccharomyces cerevisiae
ComponentsGlutaredoxin-1
KeywordsOXIDOREDUCTASE / Glutaredoxin 1 / yeast Saccharomyces cerevisiae
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
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsMaghool, S. / Maher, J.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140102746 Australia
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: High-resolution crystal structure of the reduced Grx1 from Saccharomyces cerevisiae.
Authors: Maghool, S. / La Fontaine, S. / Maher, M.J.
History
DepositionOct 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9022
Polymers12,8061
Non-polymers961
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.364, 51.779, 57.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12805.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: GRX1, YCL035C, YCL35C / Production host: Escherichia coli (E. coli) / References: UniProt: P25373
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.23 M Lithium sulfate monohydrate, 0.1 M Bis-Tris, pH 5.8, 26% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953654 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953654 Å / Relative weight: 1
ReflectionResolution: 1.22→41.36 Å / Num. obs: 37323 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.056 / Net I/σ(I): 19.4
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.319 / Num. unique obs: 1777 / CC1/2: 0.969 / Rpim(I) all: 0.107 / Rrim(I) all: 0.337 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.29data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→38.38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.727 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.035
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 1820 4.9 %RANDOM
Rwork0.1482 ---
obs0.1494 35443 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.86 Å2 / Biso mean: 13.895 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.22→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 5 122 972
Biso mean--14.83 23.28 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019872
X-RAY DIFFRACTIONr_bond_other_d0.0020.02811
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9851185
X-RAY DIFFRACTIONr_angle_other_deg0.89931890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10926.1942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.5615155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.269153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_rigid_bond_restr1.74231683
X-RAY DIFFRACTIONr_sphericity_free15.184597
X-RAY DIFFRACTIONr_sphericity_bonded6.59351695
LS refinement shellResolution: 1.22→1.251 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 134 -
Rwork0.149 2553 -
all-2687 -
obs--98.9 %

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