PDB-8udd: Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12...

ID or keywords:

Entry

Database: PDB / ID: 8udd

Title

Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12(Tetur05g05300) from Tetranychus urticae

Components

Glutathione-S-Transferase

Keywords

TRANSFERASE/SUBSTRATE / Glutathione-S-Transferase / GSH bound GST / Tetranychus urticae / TRANSFERASE / TRANSFERASE-SUBSTRATE complex

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity / 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: 2.65 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of 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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PDBx/mmCIF format	8udd.cif.gz	240.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8udd.ent.gz	151.3 KB	Display	PDB format
PDBx/mmJSON format	8udd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8udd_validation.pdf.gz	928.7 KB	Display	wwPDB validaton report
Full document	8udd_full_validation.pdf.gz	931 KB	Display
Data in XML	8udd_validation.xml.gz	20 KB	Display
Data in CIF	8udd_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ud/8udd ftp://data.pdbj.org/pub/pdb/validation_reports/ud/8udd	HTTPS FTP

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Related structure data

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

hetero molecules

53.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.492, 69.918, 118.050
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 215 / Label seq-ID: 2 - 215

Dom-ID
1
2

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

#1: Protein	Glutathione-S-Transferase Mass: 26275.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Gene: 107360608 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1K577
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.34 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1M Tris pH 8.5, and 25% w/v polyethylene glycol 3,350

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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: Aug 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.65→40 Å / Num. obs: 14919 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / CC_1/2: 0.998 / CC star: 1 / R_pim(I) all: 0.023 / R_rim(I) all: 0.061 / Net I/σ(I): 29
Reflection shell	Resolution: 2.65→2.71 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 637 / CC_1/2: 0.829 / CC star: 0.952 / R_pim(I) all: 0.297 / R_rim(I) all: 0.667 / % possible all: 86.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→35.967 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.915 / SU B: 27.259 / SU ML: 0.269 / Cross valid method: FREE R-VALUE / ESU R: 4.849 / ESU R Free: 0.353
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2617	706	4.79 %
R_work	0.2124	14033	-
all	0.215	-	-
obs	-	14739	98.933 %

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: 82.664 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.536 Å²	-0 Å²	-0 Å²
2-	-	-1.105 Å²	0 Å²
3-	-	-	1.641 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→35.967 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3424	0	40	32	3496

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	3544
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3189
X-RAY DIFFRACTION	r_angle_refined_deg	1.319	1.646	4805
X-RAY DIFFRACTION	r_angle_other_deg	0.683	1.552	7407
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.468	5	428
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.456	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.225	10	575
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.448	10	159
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	527
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3989
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	719
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	715
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.216	0.2	3015
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	1760
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1667
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	93
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	8
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.203	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.06	4.96	1721
X-RAY DIFFRACTION	r_mcbond_other	4.056	4.96	1721
X-RAY DIFFRACTION	r_mcangle_it	6.259	7.419	2146
X-RAY DIFFRACTION	r_mcangle_other	6.258	7.421	2147
X-RAY DIFFRACTION	r_scbond_it	4.582	5.071	1823
X-RAY DIFFRACTION	r_scbond_other	4.578	5.069	1822
X-RAY DIFFRACTION	r_scangle_it	6.784	7.546	2659
X-RAY DIFFRACTION	r_scangle_other	6.783	7.549	2660
X-RAY DIFFRACTION	r_lrange_it	10.201	57.45	3970
X-RAY DIFFRACTION	r_lrange_other	10.203	57.447	3970
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.129	0.05	6307

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	0.12917	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12917	0.05007

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
2.65-2.718	0.495	38	0.378	941	0.382	1082	0.928	0.943	90.4806	0.353
2.718-2.792	0.326	48	0.296	990	0.298	1054	0.964	0.964	98.482	0.263
2.792-2.873	0.366	51	0.256	968	0.261	1024	0.944	0.967	99.5117	0.227
2.873-2.961	0.316	42	0.247	934	0.25	978	0.947	0.966	99.7955	0.21
2.961-3.057	0.242	44	0.244	930	0.244	974	0.963	0.965	100	0.214
3.057-3.164	0.339	48	0.251	894	0.256	942	0.932	0.959	100	0.22
3.164-3.282	0.301	39	0.251	837	0.253	876	0.95	0.961	100	0.225
3.282-3.415	0.314	42	0.245	830	0.249	873	0.946	0.967	99.8855	0.223
3.415-3.565	0.254	35	0.223	804	0.224	844	0.96	0.975	99.4076	0.209
3.565-3.738	0.287	41	0.212	744	0.216	793	0.954	0.974	98.9912	0.196
3.738-3.937	0.309	38	0.212	734	0.217	772	0.942	0.972	100	0.198
3.937-4.173	0.226	41	0.174	689	0.176	730	0.972	0.982	100	0.168
4.173-4.457	0.159	33	0.153	648	0.154	681	0.986	0.985	100	0.152
4.457-4.808	0.206	32	0.152	610	0.154	643	0.972	0.985	99.8445	0.154
4.808-5.257	0.246	25	0.168	565	0.171	594	0.968	0.982	99.3266	0.17
5.257-5.862	0.259	24	0.217	529	0.219	553	0.961	0.973	100	0.223
5.862-6.739	0.282	24	0.243	457	0.245	481	0.96	0.959	100	0.248
6.739-8.182	0.239	26	0.215	397	0.216	423	0.965	0.97	100	0.23
8.182-11.283	0.194	22	0.177	324	0.178	351	0.971	0.979	98.5755	0.228
11.283-35.967	0.336	13	0.266	208	0.27	223	0.932	0.954	99.1031	0.334

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	2.9759	-0.3021	0.2939	2.6156	0.0012	4.2497	0.1691	-0.027	-0.3588	-0.0588	0.0109	-0.0614	1.0975	0.3568	-0.18	0.5053	0.0913	-0.0967	0.3421	-0.0072	0.0596	28.785	-1.709	5.39
2	15.1631	-5.138	-8.0504	2.5726	4.0519	6.4099	-0.2744	0.6653	-0.9389	0.2945	0.2177	0.1105	0.4398	0.3117	0.0567	0.9956	-0.2735	-0.0087	0.507	0.0487	0.5647	6.901	-7.945	7.331
3	2.4898	-0.3704	-0.0049	4.618	-1.0402	4.8784	0.1121	0.5625	-0.2967	-0.297	-0.0519	0.5686	0.7944	-0.4226	-0.0602	0.371	-0.0486	-0.1037	0.4352	-0.079	0.1164	15.058	3.049	-5.132
4	4.0277	-1.2349	0.2953	1.3838	-0.3779	2.8977	-0.0602	-0.5512	0.0445	0.3422	0.2487	0.0413	-0.0662	-0.2667	-0.1884	0.3034	-0.0337	-0.0039	0.4065	0.0146	0.0164	13.239	14.239	18.677
5	3.2643	5.0566	3.5803	7.8713	5.5716	3.9586	0.2663	0.2665	-0.4243	0.5865	0.266	-0.6287	0.4226	0.1381	-0.5323	1.2968	-0.3398	0.1717	1.0779	0.3112	0.6306	12.343	-9.002	22.492
6	4.8554	-1.1189	-1.6792	4.1188	-0.3803	4.4206	-0.4216	-1.1717	-0.3403	0.8317	0.4162	0.1699	0.6189	0.1932	0.0054	0.6891	0.1234	-0.0559	0.7313	0.0698	0.0475	21.899	3.934	30.653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 109
2	X-RAY DIFFRACTION	2	ALL	A	110 - 132
3	X-RAY DIFFRACTION	3	ALL	A	133 - 223

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