PDB-9sn8: Crystal structure of anthocyanin-related glutathione transferase ...

ID or keywords:

Entry

Database: PDB / ID: 9sn8

Title

Crystal structure of anthocyanin-related glutathione transferase from bilberry

Components

glutathione transferase

Keywords

TRANSFERASE / glutathione / glutathione transferase / anthocyanin / cyanidin / bilberry

Biological species

Vaccinium myrtillus (common bilberry)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 Å

Authors

Didierjean, C. / Favier, F. / Mathiot, S.

Funding support

France, 1items

Citation

Journal: 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

Deposition	Sep 10, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2026	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9sn8.cif.gz	271.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9sn8.ent.gz	214.5 KB	Display	PDB format
PDBx/mmJSON format	9sn8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sn/9sn8 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/9sn8	HTTPS FTP

-
Related structure data

Related structure data	9sn7C 9sn9C C: citing same article (ref.)

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (1)

Deposited unit

A: glutathione transferase

B: glutathione transferase

C: glutathione transferase

D: glutathione transferase

E: glutathione transferase

F: glutathione transferase

hetero molecules

147 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: glutathione transferase

B: glutathione transferase

hetero molecules

defined by author&software
Evidence: gel filtration
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: glutathione transferase

D: glutathione transferase

hetero molecules

defined by author&software
Evidence: gel filtration
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: glutathione transferase

F: glutathione transferase

hetero molecules

defined by author&software
Evidence: gel filtration
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.294, 159.117, 90.374
Angle α, β, γ (deg.)	90, 95.601, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: VAL / Beg label comp-ID: VAL

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	A	A	2 - 211	2 - 211
2	1	1	LEU	LEU	B	B	2 - 211	2 - 211
3	2	2	MET	MET	A	A	2 - 212	2 - 212
4	2	2	MET	MET	C	C	2 - 212	2 - 212
5	3	3	LEU	LEU	A	A	2 - 211	2 - 211
6	3	3	LEU	LEU	D	D	2 - 211	2 - 211
7	4	4	MET	MET	A	A	2 - 212	2 - 212
8	4	4	MET	MET	E	E	2 - 212	2 - 212
9	5	5	LEU	LEU	A	A	2 - 211	2 - 211
10	5	5	LEU	LEU	F	F	2 - 211	2 - 211
11	6	6	LEU	LEU	B	B	2 - 211	2 - 211
12	6	6	LEU	LEU	C	C	2 - 211	2 - 211
13	7	7	ASP	ASP	B	B	2 - 213	2 - 213
14	7	7	ASP	ASP	D	D	2 - 213	2 - 213
15	8	8	LEU	LEU	B	B	2 - 211	2 - 211
16	8	8	LEU	LEU	E	E	2 - 211	2 - 211
17	9	9	MET	MET	B	B	2 - 212	2 - 212
18	9	9	MET	MET	F	F	2 - 212	2 - 212
19	10	10	LEU	LEU	C	C	2 - 211	2 - 211
20	10	10	LEU	LEU	D	D	2 - 211	2 - 211
21	11	11	MET	MET	C	C	2 - 212	2 - 212
22	11	11	MET	MET	E	E	2 - 212	2 - 212
23	12	12	LEU	LEU	C	C	2 - 211	2 - 211
24	12	12	LEU	LEU	F	F	2 - 211	2 - 211
25	13	13	LEU	LEU	D	D	2 - 211	2 - 211
26	13	13	LEU	LEU	E	E	2 - 211	2 - 211
27	14	14	MET	MET	D	D	2 - 212	2 - 212
28	14	14	MET	MET	F	F	2 - 212	2 - 212
29	15	15	LEU	LEU	E	E	2 - 211	2 - 211
30	15	15	LEU	LEU	F	F	2 - 211	2 - 211

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	glutathione transferase Mass: 24528.400 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinium myrtillus (common bilberry) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.37 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion Details: Precipitating solution : - 20% v/v Ethylene glycol / 10 % w/v PEG 8000 - 0,1 M Buffer System 1 pH 6,5 (Buffer System 1 : 1.0M, pH6.5 -> Imidazole; MES monohydrate (acid)) - 0,1 M Amino acids ...Details: Precipitating solution : - 20% v/v Ethylene glycol / 10 % w/v PEG 8000 - 0,1 M Buffer System 1 pH 6,5 (Buffer System 1 : 1.0M, pH6.5 -> Imidazole; MES monohydrate (acid)) - 0,1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine) Protein solution : 14.9 mg/mL protein in 20 mM Tris-HCl pH 8.0 ; 200 mM NaCl ; 1mM EDTA

Crystal

Density Matthews: 2.76 Å³/Da / Density % sol: 55.37 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion
Details: Precipitating solution : - 20% v/v Ethylene glycol / 10 % w/v PEG 8000 - 0,1 M Buffer System 1 pH 6,5 (Buffer System 1 : 1.0M, pH6.5 -> Imidazole; MES monohydrate (acid)) - 0,1 M Amino acids ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.967697 Å / Relative weight: 1
Reflection	Resolution: 2.34→89.94 Å / Num. obs: 65742 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC_1/2: 0.992 / R_merge(I) obs: 0.105 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.34→2.4 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.637 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4594 / CC_1/2: 0.612 / % possible all: 99

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.34→89.94 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.924 / SU B: 9.586 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.362 / ESU R Free: 0.238 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2426	3282	4.995 %
R_work	0.2103	62424	-
all	0.212	-	-
obs	-	65706	98.72 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.692 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.767 Å²	-0 Å²	-1.228 Å²
2-	-	0.502 Å²	0 Å²
3-	-	-	0.496 Å²

Refinement step

Cycle: LAST / Resolution: 2.34→89.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10259	0	6	253	10518

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	10481
X-RAY DIFFRACTION	r_angle_refined_deg	1.854	1.839	14183
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.339	5	1266
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.193	5	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.848	10	1897
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.788	10	496
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	1565
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7950
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	4286
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	7140
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	360
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.259	0.2	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.184	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	5.76	4.746	5076
X-RAY DIFFRACTION	r_mcangle_it	8.816	8.52	6335
X-RAY DIFFRACTION	r_scbond_it	7.076	4.974	5405
X-RAY DIFFRACTION	r_scangle_it	10.57	8.965	7847
X-RAY DIFFRACTION	r_lrange_it	12.873	52.251	15288
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	6779
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.076	0.05	6854
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.076	0.05	6827
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.079	0.05	6842
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	6791
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.076	0.05	6795
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.08	0.05	6882
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.069	0.05	6823
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.074	0.05	6844
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.067	0.05	6855
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.074	0.05	6857
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.066	0.05	6851
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.075	0.05	6810
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.07	0.05	6914
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.073	0.05	6815

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07625	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07625	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07634	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07634	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07557	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07557	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07888	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.07888	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0787	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.0787	0.05009
6	11	B	X-RAY DIFFRACTION	Local ncs	0.07644	0.05009
6	12	C	X-RAY DIFFRACTION	Local ncs	0.07644	0.05009
7	13	B	X-RAY DIFFRACTION	Local ncs	0.07961	0.0501
7	14	D	X-RAY DIFFRACTION	Local ncs	0.07961	0.0501
8	15	B	X-RAY DIFFRACTION	Local ncs	0.06905	0.05009
8	16	E	X-RAY DIFFRACTION	Local ncs	0.06905	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.07403	0.05009
9	18	F	X-RAY DIFFRACTION	Local ncs	0.07403	0.05009
10	19	C	X-RAY DIFFRACTION	Local ncs	0.06742	0.0501
10	20	D	X-RAY DIFFRACTION	Local ncs	0.06742	0.0501
11	21	C	X-RAY DIFFRACTION	Local ncs	0.07384	0.05009
11	22	E	X-RAY DIFFRACTION	Local ncs	0.07384	0.05009
12	23	C	X-RAY DIFFRACTION	Local ncs	0.06553	0.05009
12	24	F	X-RAY DIFFRACTION	Local ncs	0.06553	0.05009
13	25	D	X-RAY DIFFRACTION	Local ncs	0.07484	0.05009
13	26	E	X-RAY DIFFRACTION	Local ncs	0.07484	0.05009
14	27	D	X-RAY DIFFRACTION	Local ncs	0.07047	0.05009
14	28	F	X-RAY DIFFRACTION	Local ncs	0.07047	0.05009
15	29	E	X-RAY DIFFRACTION	Local ncs	0.07258	0.05009
15	30	F	X-RAY DIFFRACTION	Local ncs	0.07258	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.34-2.401	0.33	245	0.306	4572	X-RAY DIFFRACTION	98.932
2.401-2.466	0.326	250	0.293	4504	X-RAY DIFFRACTION	99.0004
2.466-2.538	0.311	230	0.273	4387	X-RAY DIFFRACTION	99.0348
2.538-2.616	0.308	203	0.275	4250	X-RAY DIFFRACTION	99.1318
2.616-2.702	0.287	191	0.246	4215	X-RAY DIFFRACTION	99.5481
2.702-2.796	0.258	214	0.23	3972	X-RAY DIFFRACTION	99.5482
2.796-2.902	0.254	237	0.225	3852	X-RAY DIFFRACTION	99.3199
2.902-3.02	0.295	182	0.214	3701	X-RAY DIFFRACTION	99.208
3.02-3.154	0.251	176	0.204	3572	X-RAY DIFFRACTION	98.9702
3.154-3.308	0.234	185	0.207	3245	X-RAY DIFFRACTION	94.1273
3.308-3.487	0.25	148	0.223	3034	X-RAY DIFFRACTION	92.7967
3.487-3.698	0.271	128	0.219	3111	X-RAY DIFFRACTION	99.9075
3.698-3.953	0.225	150	0.202	2887	X-RAY DIFFRACTION	99.5411
3.953-4.269	0.219	160	0.17	2686	X-RAY DIFFRACTION	99.8246
4.269-4.675	0.199	133	0.158	2494	X-RAY DIFFRACTION	99.6586
4.675-5.225	0.204	140	0.159	2228	X-RAY DIFFRACTION	99.5795
5.225-6.03	0.236	95	0.21	1995	X-RAY DIFFRACTION	99.4291
6.03-7.377	0.241	110	0.212	1664	X-RAY DIFFRACTION	99.8312
7.377-10.398	0.203	69	0.175	1311	X-RAY DIFFRACTION	99.639
10.398-89.94	0.139	36	0.214	744	X-RAY DIFFRACTION	98.8593

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi