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- PDB-8a0r: Crystal structure of poplar glutathione transferase U20 in comple... -

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Basic information

Entry
Database: PDB / ID: 8a0r
TitleCrystal structure of poplar glutathione transferase U20 in complex with pinocembrin
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / Tau / Plant
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding / cytoplasm
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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
pinocembrin / glutathione transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 30, 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)25,3724
Polymers24,9581
Non-polymers4143
Water4,089227
1
A: Glutathione transferase
hetero molecules

A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7448
Polymers49,9162
Non-polymers8286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2940 Å2
ΔGint-34 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.338, 56.338, 182.615
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glutathione transferase


Mass: 24957.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_008G175000, POPTR_1996s00210g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2X9R3, glutathione transferase
#2: Chemical ChemComp-KML / pinocembrin / (2~{S})-5,7-bis(oxidanyl)-2-phenyl-2,3-dihydrochromen-4-one


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8.5
Details: 200 mM calcium chloride, 100 mM Tris-HCl pH 8.5, 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40026 / % possible obs: 100 % / Redundancy: 27 % / Biso Wilson estimate: 33.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.5
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 5669 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A08

8a08


Resolution: 1.6→23.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.087 / SU Rfree Cruickshank DPI: 0.083
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1967 -RANDOM
Rwork0.2136 ---
obs0.2145 39907 100 %-
Displacement parametersBiso mean: 33.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.5223 Å20 Å20 Å2
2---1.5223 Å20 Å2
3---3.0446 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 28 227 1986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081838HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d639SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes315HARMONIC5
X-RAY DIFFRACTIONt_it1826HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1797SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion15.63
LS refinement shellResolution: 1.6→1.61 Å
RfactorNum. reflection% reflection
Rfree0.2769 36 -
Rwork0.2722 --
obs0.2724 799 100 %

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