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

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Basic information

Entry
Database: PDB / ID: 8awz
TitleCrystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with dinitrosyl glutathionyl iron complex (DNGIC)
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
: / GLUTATHIONE / NITRIC OXIDE / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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)56,42415
Polymers55,0532
Non-polymers1,37113
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-64 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.430, 103.760, 107.590
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 , 8 types, 605 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
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: 0.981401 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: 0.981401 Å / Relative weight: 1
ReflectionResolution: 1.549→45.36 Å / Num. obs: 82204 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.074 / Net I/σ(I): 15.04
Reflection shellResolution: 1.549→1.59 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 5668 / CC1/2: 0.58 / Rrim(I) all: 0.873

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Processing

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

6f43


Resolution: 1.549→45.357 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 4110 5 %
Rwork0.1698 78084 -
obs0.1709 82194 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.76 Å2 / Biso mean: 19.3118 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.549→45.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 155 592 4543
Biso mean--25.57 29.87 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073999
X-RAY DIFFRACTIONf_angle_d0.9015431
X-RAY DIFFRACTIONf_chiral_restr0.052578
X-RAY DIFFRACTIONf_plane_restr0.007714
X-RAY DIFFRACTIONf_dihedral_angle_d17.3392397
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5494-1.56760.30051300.2934247092
1.5676-1.58670.29851340.2743254295
1.5867-1.60680.24951380.2366261798
1.6068-1.6280.27081420.21392690100
1.628-1.65030.24731390.20932643100
1.6503-1.67380.20941420.20462707100
1.6738-1.69880.21321410.19732673100
1.6988-1.72540.22251390.18442647100
1.7254-1.75370.19181420.18412699100
1.7537-1.78390.21321410.18472672100
1.7839-1.81630.2251400.18582669100
1.8163-1.85130.21271420.18762701100
1.8513-1.88910.21551420.17872695100
1.8891-1.93010.17481410.17852679100
1.9301-1.9750.21071420.16782694100
1.975-2.02440.20131430.16812714100
2.0244-2.07920.18471410.16372680100
2.0792-2.14030.20711410.16842677100
2.1403-2.20940.19481430.15832713100
2.2094-2.28840.20211430.16312715100
2.2884-2.380.19981420.16542700100
2.38-2.48830.17841420.16472696100
2.4883-2.61950.19581430.16622727100
2.6195-2.78360.19221440.16382733100
2.7836-2.99850.17321440.16622736100
2.9985-3.30020.17421440.16432740100
3.3002-3.77750.1661450.15262755100
3.7775-4.75840.15291470.1419279999
4.7584-45.3570.19271530.1721290199

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