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- PDB-8ax0: Crystal structure of Trametes versicolor glutathione transferase ... -

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Basic information

Entry
Database: PDB / ID: 8ax0
TitleCrystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with sodium nitroprusside
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 / Nitroprusside ion / DI(HYDROXYETHYL)ETHER / 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)56,41612
Polymers55,0532
Non-polymers1,36310
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-14 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 104.310, 107.380
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, 436 molecules

#2: Chemical
ChemComp-NT3 / Nitroprusside ion


Mass: 216.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5HFeN6O / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 426 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 30% (w/v) PEG 400, 0.2 M calcium acetate in 0.1 M pH 4.5 acetate buffer (final pH of 5.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97975 Å / Relative weight: 1
ReflectionResolution: 1.65→47.74 Å / Num. obs: 67187 / % possible obs: 97.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Net I/σ(I): 19.47
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 3898 / CC1/2: 0.52 / Rrim(I) all: 1 / % possible all: 77.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F43

6f43


Resolution: 1.65→47.738 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 3356 5 %
Rwork0.1649 63759 -
obs0.1668 67115 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 26.1166 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 1.65→47.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 122 426 4344
Biso mean--40.59 33.22 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133989
X-RAY DIFFRACTIONf_angle_d1.3635440
X-RAY DIFFRACTIONf_chiral_restr0.066569
X-RAY DIFFRACTIONf_plane_restr0.011704
X-RAY DIFFRACTIONf_dihedral_angle_d16.2022373
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.67360.2661080.2665205976
1.6736-1.69860.29161160.2402219582
1.6986-1.72510.27631230.2313235488
1.7251-1.75340.23291330.2285251492
1.7534-1.78360.26721340.2159255896
1.7836-1.81610.24171420.2075268499
1.8161-1.8510.2321420.18952712100
1.851-1.88880.2361420.19392696100
1.8888-1.92990.20431420.1862700100
1.9299-1.97480.2261430.18042712100
1.9748-2.02410.21781440.17012742100
2.0241-2.07890.22331420.16692696100
2.0789-2.140.18761430.16552704100
2.14-2.20910.1951420.15412712100
2.2091-2.28810.18391440.15262727100
2.2881-2.37970.20331440.14972733100
2.3797-2.4880.18451430.14882714100
2.488-2.61910.19381440.15542752100
2.6191-2.78320.21251450.15022739100
2.7832-2.99810.18111450.15992761100
2.9981-3.29970.19181450.16562763100
3.2997-3.7770.21461460.15492772100
3.777-4.7580.16671490.14042827100
4.758-47.7380.20621550.1747293399

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