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- PDB-8ax2: Crystal structure of Trametes versicolor glutathione transferase ... -

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Basic information

Entry
Database: PDB / ID: 8ax2
TitleCrystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with glutathione and pentachloro-nitrosyl-osmate
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / glutathione transferase / GSTO / detoxification
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / OSMIUM ION / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsSchwartz, M. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-LAS-0002-01 France
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural insights into the interactions of glutathione transferases with a nitric oxide carrier and sodium nitroprusside.
Authors: Schwartz, M. / Perrot, T. / Beurton, J. / Zannini, F. / Morel-Rouhier, M. / Gelhaye, E. / Neiers, F. / Schaniel, D. / Favier, F. / Jacquot, J.P. / Leroy, P. / Clarot, I. / Boudier, A. / Didierjean, C.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2729
Polymers55,0532
Non-polymers1,2197
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-41 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.615, 104.548, 108.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione transferase / Glutathione S-transferase / Glutathione transferase Omega 3S


Mass: 27526.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E145, glutathione transferase

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Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-OS / OSMIUM ION / Osmium


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 30 % PEG 400, 0.2 M Calcium Acetate, 0.1 M Acetate Buffer, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.14356 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14356 Å / Relative weight: 1
ReflectionResolution: 1.62→50.62 Å / Num. obs: 140484 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Net I/σ(I): 26.9
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 13.3 % / Num. unique obs: 10527 / CC1/2: 0.89 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.62→37.574 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 6883 4.9 %
Rwork0.1846 133601 -
obs0.1858 140484 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.28 Å2 / Biso mean: 20.9174 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.62→37.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 101 263 4147
Biso mean--27.46 25.49 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063954
X-RAY DIFFRACTIONf_angle_d0.8085376
X-RAY DIFFRACTIONf_chiral_restr0.047572
X-RAY DIFFRACTIONf_plane_restr0.006708
X-RAY DIFFRACTIONf_dihedral_angle_d16.9032364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6201-1.63850.34651580.3147427094
1.6385-1.65780.32482090.26814443100
1.6578-1.6780.26512050.24324510100
1.678-1.69930.2392200.20934416100
1.6993-1.72160.23912410.19064485100
1.7216-1.74520.17911920.18514554100
1.7452-1.77010.21631940.19414436100
1.7701-1.79660.22942330.19514483100
1.7966-1.82460.22562480.19414446100
1.8246-1.85450.23522660.19564401100
1.8545-1.88650.22652470.20644482100
1.8865-1.92080.21332860.19534366100
1.9208-1.95780.22022530.1844490100
1.9578-1.99770.20922210.18244452100
1.9977-2.04120.17322300.17894460100
2.0412-2.08860.23742740.18874449100
2.0886-2.14090.23382160.18494452100
2.1409-2.19870.21892160.17824491100
2.1987-2.26340.19082690.17764426100
2.2634-2.33650.2122510.17564430100
2.3365-2.420.20122410.18694492100
2.42-2.51690.20372550.1914440100
2.5169-2.63140.21471800.19294504100
2.6314-2.77010.21411890.18684494100
2.7701-2.94360.22852000.19794495100
2.9436-3.17070.21932230.20164494100
3.1707-3.48960.21632540.19894413100
3.4896-3.99410.19692630.16264434100
3.9941-5.03020.17042370.15124469100
5.0302-37.5740.17292120.167442499

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