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- PDB-8ax1: Crystal structure of Trametes versicolor glutathione transferase ... -

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Basic information

Entry
Database: PDB / ID: 8ax1
TitleCrystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with hydroxy-tetranitro-nitrosyl-ruthenate
ComponentsGlutathione transferase
KeywordsTRANSFERASE / glutathione transferase / GSTO / detoxification
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / 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
ACETATE ION / tetranitro-nitroso-oxidanyl-ruthenium(2-) / RUTHENIUM ION / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,76611
Polymers55,0532
Non-polymers1,7139
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-17 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.590, 104.590, 108.170
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 transferase Omega 3S


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

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Non-polymers , 6 types, 409 molecules

#2: Chemical
ChemComp-ODU / tetranitro-nitroso-oxidanyl-ruthenium(2-) / hydroxy-tetranitro-nitrosyl-ruthenate


Mass: 332.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HN5O10Ru / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ru
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
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: 0.9814 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 1.65→47.09 Å / Num. obs: 69693 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.073 / Net I/σ(I): 16.9
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 5091 / CC1/2: 0.74 / Rrim(I) all: 0.884 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F43

6f43


Resolution: 1.65→28.71 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 3484 5 %
Rwork0.1779 66195 -
obs0.179 69679 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.21 Å2 / Biso mean: 25.3183 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.65→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 102 400 4289
Biso mean--40.41 32.82 -
Num. residues----480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.26031360.24632589272599
1.67-1.70.23371370.23726052742100
1.7-1.720.29751380.22826122750100
1.72-1.750.2411380.221526232761100
1.75-1.780.24741380.21526182756100
1.78-1.810.20821400.205426562796100
1.81-1.840.22321350.202425732708100
1.84-1.880.21821390.198426512790100
1.88-1.910.25741370.225952732100
1.91-1.960.21121390.188826412780100
1.96-20.21281390.184526302769100
2-2.050.21461370.17826182755100
2.05-2.110.2191400.181126482788100
2.11-2.170.20961380.173726352773100
2.17-2.240.18431390.161326322771100
2.24-2.320.20741390.164426412780100
2.32-2.410.18251390.160326472786100
2.41-2.520.16891400.161626532793100
2.52-2.650.18681390.167826532792100
2.65-2.820.1891400.163626532793100
2.82-3.040.22361410.182926732814100
3.04-3.340.19291410.189526812822100
3.34-3.830.19881420.16726912833100
3.83-4.820.16861430.14952724286799
4.82-28.710.19181500.19432853300399

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