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- PDB-9sn7: Crystal structure of anthocyanin-related glutathione transferase ... -

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Basic information

Entry
Database: PDB / ID: 9sn7
TitleCrystal structure of anthocyanin-related glutathione transferase from poplar in complex with quercetin
Componentsglutathione transferase
KeywordsTRANSFERASE / glutathione / glutathione transferase / anthocyanin / cyanidin / poplar / quercetin
Function / homology
Function and homology information


toxin catabolic process / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / 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
GLUTATHIONE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / glutathione transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDidierjean, C. / Favier, F. / Mathiot, S.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural and biochemical insights into an anthocyanin-related glutathione transferase from bilberry and its inhibition by quercetin.
Authors: Morette, L. / Mathiot, S. / Rochoux, S. / Schwander, T. / Schwartz, M. / Nguyen, H.M. / Favier, F. / Buller, R. / Hecker, A. / Didierjean, C.
History
DepositionSep 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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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)24,9493
Polymers24,3401
Non-polymers6102
Water2,324129
1
A: glutathione transferase
hetero molecules

A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8996
Polymers48,6802
Non-polymers1,2194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)89.639, 55.412, 54.894
Angle α, β, γ (deg.)90, 119.812, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein glutathione transferase


Mass: 24339.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_017G138800 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MWW0, glutathione transferase
#2: Chemical ChemComp-GSH / Glutathione


Type: peptide-like / Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: microbatch
Details: Precipitating solution : - 25 % w/v PEG 4000 - 100 mM MES pH 6.5 - 200 mM MgCl2 Protein solution : 10mg/ml protein in 20 mM Tris pH 8.0 - 5mM DTT - 10mM L-Cystein - 2.1mM Quercetin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.4→47.63 Å / Num. obs: 43970 / % possible obs: 95.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Net I/σ(I): 22.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.7 % / Num. unique obs: 1748 / CC1/2: 0.913 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.629 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.776 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.054 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1724 2267 5.158 %
Rwork0.1424 41681 -
all0.144 --
obs-43948 95.5 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.035 Å2-0 Å20.612 Å2
2---1.193 Å2-0 Å2
3---0.318 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 42 129 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121858
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.8362531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.01513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35710331
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2991090
X-RAY DIFFRACTIONr_chiral_restr0.1230.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021476
X-RAY DIFFRACTIONr_nbd_refined0.2150.2815
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.213
X-RAY DIFFRACTIONr_mcbond_it6.1961.955869
X-RAY DIFFRACTIONr_mcangle_it8.6053.5261089
X-RAY DIFFRACTIONr_scbond_it8.4262.237989
X-RAY DIFFRACTIONr_scangle_it11.57541433
X-RAY DIFFRACTIONr_lrange_it13.64821.6762834
X-RAY DIFFRACTIONr_rigid_bond_restr5.48531858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.5650.1856110.135114670.137130240.9690.98792.73650.106
1.565-1.8070.1616770.103105630.107114700.9830.99397.99480.088
1.807-2.2120.1744610.12990110.13197360.9810.9997.28840.123
2.212-3.1250.1793140.15268750.15375500.9810.98595.21850.16
3.125-47.6290.1682040.16437590.16442320.9830.98393.64370.195

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