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- PDB-9sn9: Crystal structure of anthocyanin-related glutathione transferase ... -

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Basic information

Entry
Database: PDB / ID: 9sn9
TitleCrystal structure of anthocyanin-related glutathione transferase from bilberry in complex with glutathione
Componentsglutathione transferase
KeywordsTRANSFERASE / glutathione / glutathione transferase / anthocyanin / cyanidin / bilberry
Function / homologyGLUTATHIONE
Function and homology information
Biological speciesVaccinium myrtillus (common bilberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9317
Polymers49,0572
Non-polymers8745
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-69 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.881, 82.904, 91.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 211 / Label seq-ID: 2 - 211

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein glutathione transferase


Mass: 24528.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinium myrtillus (common bilberry) / Production host: Escherichia coli (E. coli) / References: glutathione transferase
#2: Chemical ChemComp-GSH / Glutathione


Type: peptide-like / Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Precipitating solution : - 25% PEG 4000 - 10% MPD 10% - 100 mM MES pH 6.5 Protein solution : - 10 mg/mL protein in Tris-HCl 30 mM pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.979506 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979506 Å / Relative weight: 1
ReflectionResolution: 1.8→47.72 Å / Num. obs: 39704 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2299 / CC1/2: 0.63 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.802→47.715 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.521 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2145 1960 4.942 %
Rwork0.1709 37699 -
all0.173 --
obs-39659 98.888 %
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: 21.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.521 Å2-0 Å2-0 Å2
2---1.528 Å20 Å2
3---2.048 Å2
Refinement stepCycle: LAST / Resolution: 1.802→47.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 57 215 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163439
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.654803
X-RAY DIFFRACTIONr_angle_other_deg0.661.5757900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.535532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.810632
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.86210166
X-RAY DIFFRACTIONr_chiral_restr0.1080.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2270.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23125
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21720
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2192
X-RAY DIFFRACTIONr_metal_ion_refined0.090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.212
X-RAY DIFFRACTIONr_nbd_other0.2350.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.26
X-RAY DIFFRACTIONr_mcbond_it2.6131.9971695
X-RAY DIFFRACTIONr_mcbond_other2.6081.9971695
X-RAY DIFFRACTIONr_mcangle_it3.353.5752117
X-RAY DIFFRACTIONr_mcangle_other3.3493.5762118
X-RAY DIFFRACTIONr_scbond_it4.3162.4321855
X-RAY DIFFRACTIONr_scbond_other4.3152.4331856
X-RAY DIFFRACTIONr_scangle_it6.3124.2432686
X-RAY DIFFRACTIONr_scangle_other6.3114.2442687
X-RAY DIFFRACTIONr_lrange_it7.73920.4144032
X-RAY DIFFRACTIONr_lrange_other7.71920.0483983
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.056804
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.111010.05008
12AX-RAY DIFFRACTIONLocal ncs0.111010.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.802-1.8480.2891420.26627430.26729160.9290.93498.93690.237
1.848-1.8990.3011390.27526820.27628350.9140.93199.50620.234
1.899-1.9540.2741320.22126290.22327930.9340.95698.85430.181
1.954-2.0140.281230.21225080.21526730.950.96198.42870.171
2.014-2.080.2321150.19624630.19826300.9630.9798.02280.159
2.08-2.1530.2311070.18724140.18925260.9640.97399.80210.151
2.153-2.2340.2471140.17923240.18224450.9560.97799.71370.148
2.234-2.3250.1931220.16222150.16423560.9740.98199.19360.134
2.325-2.4280.2151190.15321170.15622730.9720.98398.37220.127
2.428-2.5460.2231040.16520160.16821530.9650.98198.46730.138
2.546-2.6830.182880.15119880.15320830.9780.98599.66390.129
2.683-2.8450.2161150.15618140.15919390.9690.98499.48430.133
2.845-3.0410.271850.17517520.17918500.9570.9899.29730.155
3.041-3.2840.175870.15116100.15217410.9790.98597.47270.144
3.284-3.5950.203990.15914940.16215990.9750.98499.62480.153
3.595-4.0170.178670.15113780.15214600.9820.98798.97260.153
4.017-4.6330.186570.13412120.13612960.980.98997.91670.137
4.633-5.6610.213730.15510280.15811150.9810.98898.74440.155
5.661-7.950.173420.1698250.178810.9860.98698.41090.165
7.95-47.7150.149300.1454870.1465400.9860.98495.74070.163

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