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- PDB-7zvp: Crystal structure of poplar glutathione transferase U19 in comple... -

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Basic information

Entry
Database: PDB / ID: 7zvp
TitleCrystal structure of poplar glutathione transferase U19 in complex with glutathione
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / Tau
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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 / S-Hydroxy-Glutathione / Glutathione S-transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsDidierjean, C. / Favier, F.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Front Mol Biosci / Year: 2022
Title: Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids.
Authors: Sylvestre-Gonon, E. / Morette, L. / Viloria, M. / Mathiot, S. / Boutilliat, A. / Favier, F. / Rouhier, N. / Didierjean, C. / Hecker, A.
History
DepositionMay 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4954
Polymers25,0541
Non-polymers4413
Water4,630257
1
A: Glutathione transferase
hetero molecules

A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9918
Polymers50,1082
Non-polymers8836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3450 Å2
ΔGint-19 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.727, 56.727, 182.015
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

#1: Protein Glutathione transferase


Mass: 25053.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_008G174900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9HKX9, glutathione transferase
#2: Chemical ChemComp-GS8 / S-Hydroxy-Glutathione


Mass: 323.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate pH 6.5 and 18 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.61→48.1 Å / Num. obs: 39646 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.7
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1927 / CC1/2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZS3

7zs3


Resolution: 1.61→48.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 1895 -RANDOM
Rwork0.2291 ---
obs0.2301 39549 99.8 %-
Displacement parametersBiso mean: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.6978 Å20 Å20 Å2
2---2.6978 Å20 Å2
3---5.3956 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.61→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 29 257 2032
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081865HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882536HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d659SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes321HARMONIC5
X-RAY DIFFRACTIONt_it1865HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1939SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.11
LS refinement shellResolution: 1.61→1.62 Å
RfactorNum. reflection% reflection
Rfree0.2557 33 -
obs--100 %

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