PDB-3vk9: Crystal structure of delta-class glutathione transferase from silkmoth

ID or keywords:

Entry

Database: PDB / ID: 3vk9

Title

Crystal structure of delta-class glutathione transferase from silkmoth

Components

Glutathione S-transferase delta

Keywords

TRANSFERASE /

glutathione binding

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Bombyx mori (domestic silkworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.001 Å

Authors

Kakuta, Y. / Usuda, K. / Higashiura, A. / Suzuki, M. / Nakagawa, A. / Kimura, M. / Yamamoto, K.

Citation

Journal: Biochim.Biophys.Acta / Year: 2012
Title: Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase
Authors: Yamamoto, K. / Usuda, K. / Kakuta, Y. / Kimura, M. / Higashiura, A. / Nakagawa, A. / Aso, Y. / Suzuki, M.

History

Deposition	Nov 10, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3vk9.cif.gz	351.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3vk9.ent.gz	291.4 KB	Display	PDB format
PDBx/mmJSON format	3vk9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/3vk9 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/3vk9	HTTPS FTP

-
Related structure data

Similar structure data	5f07-1 3gh6-1 4ec0-d 1bye-1 5f05-2 6f01-d 3f6f-1 1r5a-1 4ri7-d 4e8h-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (9) #255 - Mar 2021 Cisplatin and DNA similarity (7)

Deposited unit

A: Glutathione S-transferase delta

B: Glutathione S-transferase delta

C: Glutathione S-transferase delta

D: Glutathione S-transferase delta

hetero molecules

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

1

A: Glutathione S-transferase delta

hetero molecules

A: Glutathione S-transferase delta

hetero molecules

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

2

B: Glutathione S-transferase delta

hetero molecules

B: Glutathione S-transferase delta

hetero molecules

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

3

C: Glutathione S-transferase delta

D: Glutathione S-transferase delta

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.393, 162.184, 86.791
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-244- HOH
2	1	B-243- HOH
3	1	B-347- HOH

#1: Protein	Glutathione S-transferase delta Mass: 24255.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: GST delta / Production host: Escherichia coli (E. coli) / References: UniProt: Q60GK5, glutathione transferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.001→32.1 Å / Num. obs: 60864 / B_iso Wilson estimate: 18.66 Å²

-
Processing

Software

Name	Version	Classification
BSS		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.001→31.449 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8295 / SU ML: 0.62 / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2449	3057	5.03 %
R_work	0.1885	-	-
obs	0.1913	60818	99.23 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.828 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 110.64 Å² / B_iso mean: 23.3804 Å² / B_iso min: 5.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1527 Å²	0 Å²	0 Å²
2-	-	-0.567 Å²	-0 Å²
3-	-	-	0.4143 Å²

Refinement step

Cycle: LAST / Resolution: 2.001→31.449 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6786	0	48	376	7210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7116
X-RAY DIFFRACTION	f_angle_d	1.034	9675
X-RAY DIFFRACTION	f_chiral_restr	0.072	1083
X-RAY DIFFRACTION	f_plane_restr	0.005	1230
X-RAY DIFFRACTION	f_dihedral_angle_d	13.407	2690

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.001-2.0323	0.3294	130	0.2328	2572	2702	98
2.0323-2.0656	0.2935	143	0.2365	2622	2765	100
2.0656-2.1012	0.2991	157	0.238	2575	2732	100
2.1012-2.1394	0.3147	146	0.2112	2606	2752	100
2.1394-2.1806	0.2833	129	0.2159	2631	2760	100
2.1806-2.2251	0.2764	148	0.2099	2594	2742	100
2.2251-2.2734	0.2748	115	0.2061	2631	2746	100
2.2734-2.3263	0.2597	133	0.1946	2626	2759	100
2.3263-2.3845	0.2486	158	0.1938	2610	2768	100
2.3845-2.4489	0.2915	134	0.1845	2611	2745	100
2.4489-2.5209	0.2307	126	0.1925	2653	2779	100
2.5209-2.6023	0.2805	152	0.195	2603	2755	100
2.6023-2.6952	0.2577	150	0.2008	2622	2772	100
2.6952-2.8031	0.25	147	0.1945	2627	2774	99
2.8031-2.9306	0.2482	133	0.2035	2621	2754	100
2.9306-3.0849	0.2601	145	0.1902	2620	2765	100
3.0849-3.278	0.2523	141	0.1897	2632	2773	99
3.278-3.5308	0.2256	136	0.1761	2634	2770	99
3.5308-3.8856	0.2204	146	0.1679	2622	2768	98
3.8856-4.4465	0.1889	139	0.1561	2643	2782	98
4.4465-5.5969	0.1954	128	0.1561	2671	2799	98
5.5969-31.4526	0.2048	121	0.1893	2735	2856	96

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	0.9244	-0.3249	0.2104	0.9554	-1.4639	2.9739	-0.0037	-0.0548	0.0444	0.1635	-0.0393	-0.0982	-0.0919	0.1195	0.0254	0.0875	0.0008	-0.0153	0.1064	-0.0116	0.0803	17.8729	60.2319	24.4621
2	0.8068	0.0041	-0.0008	1.2527	0.3475	0.9809	0.0365	0.0553	-0.0626	-0.1168	0.008	-0.1002	0.0707	0.0453	-0.0367	0.0718	0.0054	-0.0035	0.1003	0.0061	0.0468	5.3775	56.4608	9.9979
3	1.9262	1.1272	-0.2821	1.0685	-1.5269	4.5766	0.0377	0.1483	0.0948	-0.0924	-0.1328	-0.1344	0.1051	0.2345	0.0488	0.0918	-0.0018	0.0579	0.1514	0.0218	0.2069	17.292	-19.9342	24.8617
4	0.4159	0.501	-0.2608	1.3084	-1.6295	2.5998	-0.0209	0.2038	0.0897	-0.0565	-0.233	-0.2294	-0.0144	0.3587	0.1655	0.1474	-0.0197	0.0062	0.1897	0.0779	0.2643	22.3726	-18.5878	21.4725
5	1.3174	0.5779	-0.1224	2.2169	-1.3632	3.4327	-0.0939	0.0747	-0.1105	-0.1762	0.0335	-0.0487	-0.0195	0.153	0.0471	0.1022	0.0098	0.0818	0.1452	0.0443	0.26	15.5776	-16.7006	12.0869
6	1.4177	-0.1867	-0.3345	0.094	-0.0464	0.8525	-0.032	-0.1386	-0.0126	-0.014	-0.1357	-0.0348	0.187	-0.0059	0.0391	0.1288	-0.0283	0.0378	0.1211	0.005	0.228	6.5985	-30.2337	24.8275
7	0.4859	0.5895	0.2888	1.3638	-0.0505	0.8343	0.0648	-0.1331	0.2387	0.1316	-0.0723	0.1451	0.0292	-0.1394	0.1047	0.0806	-0.0153	0.0643	0.1561	-0.0621	0.2939	-2.4414	-22.0118	28.058
8	0.9572	0.9014	0.5124	1.153	0.2811	0.4121	-0.0542	0.0162	0.5536	-0.0534	-0.0618	0.0316	-0.2344	0.1504	-0.0236	0.2152	-0.0619	0.0439	0.2109	-0.0291	0.8409	6.3882	-1.0401	27.4684
9	0.3745	0.0307	-0.0517	0.5723	-0.1555	0.0965	0.1006	-0.1203	0.4218	0.0806	-0.0596	0.2007	-0.1033	0.01	-0.0811	0.1887	-0.0407	0.1574	0.2411	-0.2867	0.6695	-2.7817	-5.8607	35.7898
10	0.398	0.3832	0.3833	0.6414	0.242	0.4427	0.1502	-0.4571	0.6103	0.3038	-0.1464	0.0616	0.0012	-0.1202	0.0719	0.1662	-0.0573	0.1241	0.264	-0.1461	0.395	5.5134	-16.1375	39.5199
11	1.6358	0.8613	0.0913	5.668	-0.8814	1.0969	0.0557	-0.0395	0.5521	0.1712	-0.1219	-0.0568	-0.1101	0.0467	0.0565	0.1543	0.0004	0.0481	0.169	-0.0396	0.3443	19.0788	-10.2005	33.54
12	2.2631	-0.0864	-0.5678	2.5037	-0.5633	3.0577	0.0013	-0.1052	-0.1943	-0.0896	0.0107	-0.0426	0.201	0.0623	-0.0037	0.0926	0.0118	-0.0022	0.0531	-0.0209	0.1055	40.4298	1.3221	21.2056
13	4.6203	1.0497	-1.0056	2.7833	0.0515	2.9832	0.0907	-0.2304	-0.1727	0.4957	-0.066	0.0501	0.1419	0.0652	-0.0388	0.148	0.0208	0.0239	0.1065	0.0326	0.1214	36.8081	5.7987	31.8595
14	1.6848	-0.0473	-0.0164	1.1879	-0.2704	1.3114	-0.0645	0.0529	-0.053	-0.0526	0.0329	-0.1609	-0.0332	0.2397	0.0132	0.0978	0.0019	0.0008	0.1107	0.0005	0.1095	47.315	17.6814	17.3677
15	3.4147	1.6295	-0.0472	3.7538	-0.5219	2.0919	-0.0542	-0.0758	-0.3175	0.1904	-0.0749	0.1497	0.2173	-0.2367	0.1632	0.1613	-0.0401	0.0636	0.1612	-0.004	0.146	21.6893	14.1739	15.0107
16	6.7399	0.4915	-1.8346	1.6612	0.4451	1.8307	0.0439	0.2527	0.2493	-0.1364	0.0146	0.2356	-0.2518	-0.1626	-0.0662	0.122	-0.0017	-0.0306	0.1345	0.009	0.0877	26.3474	22.6409	6.6048
17	1.6598	0.6158	-0.3023	1.1373	-0.5252	1.1976	0.0274	0.1185	-0.0094	-0.172	0.0173	-0.0172	0.0843	0.0843	-0.0212	0.0968	0.0122	0.0141	0.0784	0.0002	0.041	40.1734	15.1145	6.5667
18	2.5718	0.1845	-0.392	1.604	-0.5564	1.6533	-0.0614	0.1704	-0.2327	-0.3717	0.0743	0.0821	0.2422	-0.1952	-0.0062	0.1491	-0.0221	0.0062	0.1381	-0.0254	0.0806	33.8656	13.0389	0.663
19	4.2266	0.3249	-2.6013	1.8329	-0.6728	2.7796	0.0242	0.334	-0.4314	-0.072	0.0576	0.1168	0.3223	-0.2246	-0.0078	0.203	0.0046	0.0018	0.065	-0.0192	0.086	30.3137	0.8042	10.5188
20	2.1257	-0.2683	0.7749	2.2954	-0.1523	2.112	-0.0248	0.2075	0.1223	-0.3334	0.0307	-0.0572	-0.0418	-0.0198	-0.0297	0.1501	-0.0098	-0.0191	0.1079	0.003	0.0896	38.5561	38.4279	16.6792
21	1.4097	0.1635	-0.4486	1.1726	-0.0261	1.2405	0.0067	-0.0992	-0.0077	0.1417	0.027	-0.0135	-0.0619	-0.0529	-0.0328	0.1059	0.0155	-0.0258	0.0798	0.0107	0.0514	34.8967	25.0748	32.0185
22	4.532	-1.1764	2.8676	2.8705	-0.5414	3.6064	-0.0481	-0.3313	0.4301	0.0651	0.1262	0.1069	-0.3868	-0.211	-0.0296	0.2183	0.0217	0.0112	0.0849	-0.0096	0.1067	29.4122	40.7203	31.8409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and (resseq 1:66)	A	1 - 66
2	X-RAY DIFFRACTION	2	chain A and (resseq 67:214)	A	67 - 214
3	X-RAY DIFFRACTION	3	chain B and (resseq 2:23)	B	2 - 23
4	X-RAY DIFFRACTION	4	chain B and (resseq 24:38)	B	24 - 38
5	X-RAY DIFFRACTION	5	chain B and (resseq 39:66)	B	39 - 66
6	X-RAY DIFFRACTION	6	chain B and (resseq 67:88)	B	67 - 88
7	X-RAY DIFFRACTION	7	chain B and (resseq 89:104)	B	89 - 104
8	X-RAY DIFFRACTION	8	chain B and (resseq 105:125)	B	105 - 125
9	X-RAY DIFFRACTION	9	chain B and (resseq 126:142)	B	126 - 142
10	X-RAY DIFFRACTION	10	chain B and (resseq 143:191)	B	143 - 191
11	X-RAY DIFFRACTION	11	chain B and (resseq 192:214)	B	192 - 214
12	X-RAY DIFFRACTION	12	chain C and (resseq 1:37)	C	1 - 37
13	X-RAY DIFFRACTION	13	chain C and (resseq 38:66)	C	38 - 66
14	X-RAY DIFFRACTION	14	chain C and (resseq 67:104)	C	67 - 104
15	X-RAY DIFFRACTION	15	chain C and (resseq 105:125)	C	105 - 125
16	X-RAY DIFFRACTION	16	chain C and (resseq 126:142)	C	126 - 142
17	X-RAY DIFFRACTION	17	chain C and (resseq 143:170)	C	143 - 170
18	X-RAY DIFFRACTION	18	chain C and (resseq 171:191)	C	171 - 191
19	X-RAY DIFFRACTION	19	chain C and (resseq 192:215)	C	192 - 215
20	X-RAY DIFFRACTION	20	chain D and (resseq 1:66)	D	1 - 66
21	X-RAY DIFFRACTION	21	chain D and (resseq 67:191)	D	67 - 191
22	X-RAY DIFFRACTION	22	chain D and (resseq 192:215)	D	192 - 215

-
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