PDB-8ude: Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm06...

ID or keywords:

Entry

Database: PDB / ID: 8ude

Title

Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm06(Tetur05g05220) from Tetranychus urticae

Components

Glutathione-S-Transferase

Keywords

TRANSFERASE/SUBSTRATE / Glutathione-S-Transferase / Mu class GST TuGSTm06 / GST bound to GSH / TRANSFERASE / TRANSFERASE-SUBSTRATE complex

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / identical protein binding
Similarity search - Function

Biological species

Tetranychus urticae (two-spotted spider mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Khatri, K. / Arriaza, R.H. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Mu class GST from Tetranychus urticae
Authors: Khatri, K. / Arriaza, R.H. / Chruszcz, M.

History

Deposition	Sep 28, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ude.cif.gz	493.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ude.ent.gz	316.9 KB	Display	PDB format
PDBx/mmJSON format	8ude.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ude_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8ude_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8ude_validation.xml.gz	41.9 KB	Display
Data in CIF	8ude_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ud/8ude ftp://data.pdbj.org/pub/pdb/validation_reports/ud/8ude	HTTPS FTP

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Related structure data

Related structure data	8udaC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (11) #255 - Mar 2021 Cisplatin and DNA similarity (11)

Deposited unit

A: Glutathione-S-Transferase

B: Glutathione-S-Transferase

C: Glutathione-S-Transferase

D: Glutathione-S-Transferase

hetero molecules

107 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutathione-S-Transferase

D: Glutathione-S-Transferase

hetero molecules

defined by author&software
53.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutathione-S-Transferase

C: Glutathione-S-Transferase

hetero molecules

defined by author&software
53.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.802, 135.802, 191.998
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 224 / Label seq-ID: 2 - 224

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
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

#1: Protein	Glutathione-S-Transferase Mass: 26180.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Gene: 107360789 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1K569
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2 M ammonium sulfate, 0.1 M Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→40 Å / Num. obs: 62541 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / R_pim(I) all: 0.04 / R_rim(I) all: 0.094 / Net I/σ(I): 23.9
Reflection shell	Resolution: 2.25→2.29 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3143 / CC_1/2: 0.773 / R_pim(I) all: 0.251 / R_rim(I) all: 0.586

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→39.233 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.933 / SU B: 12.345 / SU ML: 0.161 / Cross valid method: FREE R-VALUE / ESU R: 0.239 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2357	3135	5.026 %
R_work	0.1967	59239	-
all	0.199	-	-
obs	-	62374	99.523 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 63.802 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.372 Å²	0.186 Å²	-0 Å²
2-	-	0.372 Å²	0 Å²
3-	-	-	-1.208 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→39.233 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7267	0	140	412	7819

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	7571
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7095
X-RAY DIFFRACTION	r_angle_refined_deg	1.389	1.657	10240
X-RAY DIFFRACTION	r_angle_other_deg	0.745	1.573	16417
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.019	5	892
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.714	5	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.919	10	1340
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.033	10	357
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1114
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	8672
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	1676
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1536
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	6420
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	3772
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3763
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	370
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.072	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.258	0.2	30
X-RAY DIFFRACTION	r_nbd_other	0.235	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	4.841	4.824	3574
X-RAY DIFFRACTION	r_mcbond_other	4.838	4.825	3574
X-RAY DIFFRACTION	r_mcangle_it	6.053	8.667	4464
X-RAY DIFFRACTION	r_mcangle_other	6.054	8.668	4465
X-RAY DIFFRACTION	r_scbond_it	6.785	5.442	3997
X-RAY DIFFRACTION	r_scbond_other	6.485	5.37	3948
X-RAY DIFFRACTION	r_scangle_it	9.134	9.774	5776
X-RAY DIFFRACTION	r_scangle_other	8.742	9.657	5705
X-RAY DIFFRACTION	r_lrange_it	9.761	50.055	8688
X-RAY DIFFRACTION	r_lrange_other	9.775	49.878	8627
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.074	0.05	7338
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.086	0.05	7234
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.089	0.05	7164
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.08	0.05	7265
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.082	0.05	7265
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.063	0.05	7375

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	0.07406	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07406	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08648	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08648	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08904	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.08904	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08014	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08014	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08193	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08193	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06314	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06314	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.25-2.308	0.286	244	0.254	4361	0.256	4615	0.945	0.96	99.7833	0.226
2.308-2.371	0.275	249	0.231	4235	0.234	4509	0.953	0.967	99.4455	0.206
2.371-2.44	0.275	224	0.221	4109	0.223	4360	0.95	0.97	99.3807	0.194
2.44-2.515	0.264	204	0.211	4015	0.214	4253	0.952	0.972	99.2006	0.184
2.515-2.597	0.263	201	0.21	3878	0.213	4136	0.947	0.972	98.6219	0.185
2.597-2.687	0.248	212	0.193	3739	0.196	3964	0.958	0.977	99.6721	0.168
2.687-2.788	0.238	182	0.201	3712	0.203	3896	0.961	0.974	99.9487	0.178
2.788-2.902	0.253	215	0.209	3476	0.212	3693	0.956	0.972	99.9458	0.188
2.902-3.03	0.24	170	0.201	3381	0.203	3552	0.963	0.975	99.9718	0.188
3.03-3.177	0.258	162	0.219	3246	0.221	3414	0.957	0.972	99.8243	0.206
3.177-3.347	0.243	150	0.206	3057	0.207	3221	0.968	0.976	99.5654	0.198
3.347-3.549	0.232	161	0.194	2850	0.196	3044	0.969	0.979	98.9159	0.19
3.549-3.792	0.24	155	0.188	2692	0.19	2875	0.963	0.979	99.0261	0.188
3.792-4.092	0.207	105	0.181	2587	0.182	2695	0.968	0.979	99.8887	0.183
4.092-4.478	0.215	110	0.168	2334	0.17	2444	0.967	0.981	100	0.176
4.478-4.998	0.202	109	0.183	2151	0.184	2261	0.966	0.979	99.9558	0.193
4.998-5.756	0.26	100	0.188	1865	0.191	1967	0.951	0.98	99.8983	0.195
5.756-7.012	0.223	104	0.201	1555	0.203	1682	0.969	0.975	98.6326	0.217
7.012-9.762	0.159	43	0.174	1255	0.174	1303	0.987	0.983	99.6163	0.195
9.762-39.233	0.213	35	0.209	722	0.209	757	0.973	0.982	100	0.246

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.2654	-0.7834	0.0843	1.5962	0.8503	2.0938	0.1288	0.2993	-0.0799	-0.2788	-0.2061	0.1194	-0.0076	-0.0044	0.0773	0.0708	0.0341	-0.0079	0.0534	-0.0216	0.2163	-18.323	-17.758	-11.917
2	1.7076	0.9103	1.2565	2.5005	0.3996	2.9472	0.0052	-0.013	0.0965	0.0815	0.0233	-0.0185	0.1119	0.0262	-0.0285	0.0209	-0.0044	0.0424	0.0072	-0.0419	0.2592	-15.834	-17.801	6.127
3	1.674	1.0806	-0.4709	1.3579	-0.5014	2.169	-0.0956	-0.1213	-0.1501	-0.0098	-0.0005	0.032	0.2944	-0.1906	0.0961	0.0601	-0.026	0.047	0.0504	-0.0165	0.2762	-25.791	-20.433	9.857
4	1.4741	-0.4626	0.1679	3.1114	-1.0898	1.2293	0.102	0.0182	0.0156	-0.2272	-0.1016	0.447	-0.1146	-0.3054	-0.0004	0.0963	0.0684	-0.045	0.169	-0.0186	0.3573	-31.667	-13.674	0.528
5	1.9648	0.6676	-0.1682	1.7088	-0.6845	1.3866	-0.0959	0.4995	0.1494	-0.1538	0.1422	0.0028	0.0402	-0.1166	-0.0462	0.0274	-0.0105	-0.0216	0.1424	0.0309	0.2098	-7.109	-53.943	-43.78
6	2.2067	0.2308	-0.0926	3.0214	-2.2601	3.0084	-0.0592	-0.1194	-0.213	0.0068	-0.0256	-0.1801	0.3015	0.1698	0.0848	0.1073	0.0162	-0.0386	0.0489	0.0102	0.2653	-4.468	-63.655	-23.554
7	0.5616	0.1684	0.3503	1.7769	0.7826	2.6184	-0.0251	-0.0838	0.1404	0.0509	-0.0561	0.1027	-0.3154	-0.1866	0.0812	0.0573	0.0236	-0.0006	0.0212	-0.0154	0.247	-7.248	-45.854	-23.196
8	3.1643	-0.9259	-0.927	2.82	0.3424	3.0976	0.0449	0.2931	0.3579	0.0637	-0.0405	-0.2149	-0.3538	0.3271	-0.0044	0.0653	-0.0432	0.001	0.0906	0.0217	0.3057	2.43	-44.003	-31.222
9	2.7043	0.431	-0.1686	1.1003	0.395	1.6394	0.1161	-0.3879	0.1058	0.3269	-0.1708	0.0303	0.1323	-0.0554	0.0546	0.0986	-0.0491	0.0011	0.068	-0.0226	0.2052	-20.343	-62.571	-17.277
10	0.7378	-0.3575	0.4526	2.3224	0.1235	1.9473	-0.0513	0.0905	0.1442	-0.0122	0.006	0.1483	-0.2453	-0.2137	0.0453	0.0311	0.0279	0.0026	0.0627	0.0099	0.2939	-28.412	-56.619	-33.239
11	2.4467	0.0306	-1.7741	5.2033	11.4456	26.5646	-0.0835	0.0431	0.1972	0.2488	0.4308	-0.0788	0.5966	0.9632	-0.3473	0.1813	0.0773	-0.0708	0.1432	0.0056	0.2023	-35.448	-56.854	-40.148
12	2.0662	1.193	0.8754	4.1317	0.9931	3.5927	0.2488	-0.2171	0.1461	0.3673	-0.3128	0.5387	0.1987	-0.538	0.064	0.048	-0.0431	0.0671	0.0971	-0.0121	0.2988	-35.077	-63.706	-24.084
13	1.2051	-0.9774	-0.8182	2.3095	-0.8149	2.8129	-0.1919	-0.5293	-0.0949	0.2286	0.1875	-0.0142	0.2037	0.2512	0.0044	0.1033	0.011	-0.0201	0.4218	0.0603	0.294	-1.301	-31.162	18.237
14	2.0568	-1.1759	-0.3512	2.1898	-0.7925	1.9796	-0.156	-0.344	0.0928	0.2797	0.1869	0.1262	-0.0711	0.0384	-0.0309	0.0405	0.0146	0.0281	0.0827	-0.0263	0.2121	-6.12	-22.278	13.027
15	2.1611	1.9656	-2.796	3.1011	-0.6818	6.6123	-0.204	0.1866	-0.1818	-0.0484	-0.0908	0.0851	0.5022	-0.6526	0.2948	0.0982	-0.0772	0.0017	0.097	-0.0257	0.3063	-13.486	-39.874	-0.648
16	2.5871	0.4081	-0.5574	1.4492	-0.338	2.6823	0.0168	-0.1156	-0.3432	-0.1531	0.0532	-0.0729	0.3877	0.0931	-0.0699	0.0706	0.0036	-0.0111	0.015	0.0069	0.2741	2.06	-35.022	2.557

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 84
2	X-RAY DIFFRACTION	2	ALL	A	85 - 119
3	X-RAY DIFFRACTION	3	ALL	A	120 - 179
4	X-RAY DIFFRACTION	4	ALL	A	180 - 224

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