PDB-4isd: Crystal structure of GLUTATHIONE TRANSFERASE homolog from BURKHOL...

ID or keywords:

Entry

Database: PDB / ID: 4isd

Title

Crystal structure of GLUTATHIONE TRANSFERASE homolog from BURKHOLDERIA GL BGR1, TARGET EFI-501803, with bound glutathione

Components

Glutathione S-transferase

Keywords

TRANSFERASE / GST / EFI /

Structural Genomics / Enyzme Function Initiative

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Burkholderia glumae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of GLUTATHIONE TRANSFERASE homolog from BURKHOLDERIA GL BGR1, TARGET EFI-501803, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...

History

Deposition	Jan 16, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4isd.cif.gz	381.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4isd.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	4isd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/4isd ftp://data.pdbj.org/pub/pdb/validation_reports/is/4isd	HTTPS FTP

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Related structure data

Related structure data	3bbyS S: Starting model for refinement
Similar structure data	6n19-1 3wq8-1 6djg-1 6ehn-d 6w7k-2 4eac-3 5nwa-2 6dhu-1 6mz0-1 5xyh-d 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
Other databases	TargetTrack: EFI-501803

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (8) #255 - Mar 2021 Cisplatin and DNA similarity (7)

Deposited unit

A: Glutathione S-transferase

B: Glutathione S-transferase

C: Glutathione S-transferase

D: Glutathione S-transferase

E: Glutathione S-transferase

hetero molecules

128 kDa, 5 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
51.1 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
51.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Glutathione S-transferase

hetero molecules

E: Glutathione S-transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.004, 196.343, 275.360
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	E-412- HOH

#1: Protein	Glutathione S-transferase / Mass: 25236.848 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia glumae (bacteria) / Strain: BGR1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5A7Z5
#2: Chemical	ChemComp-GSH / GLUTATHIONE / Glutathione Mass: 307.323 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O

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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 Å³/Da / Density % sol: 58.99 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 7 Details: Protein (10 mM Hepes pH 7.5, 25 mM NaCl, 5 mM Reduced glutathione), Reservoir (25% Sokalan CP7, 0.1 M KCl, 0.1 M HEPES pH 7), Cryoprotection (reservoir + 20% glycerol), sitting drop vapor ...Details: Protein (10 mM Hepes pH 7.5, 25 mM NaCl, 5 mM Reduced glutathione), Reservoir (25% Sokalan CP7, 0.1 M KCl, 0.1 M HEPES pH 7), Cryoprotection (reservoir + 20% glycerol), sitting drop vapor diffusion, temperature 298K

Crystal

Density Matthews: 3 Å³/Da / Density % sol: 58.99 %

Crystal grow

Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 25 mM NaCl, 5 mM Reduced glutathione), Reservoir (25% Sokalan CP7, 0.1 M KCl, 0.1 M HEPES pH 7), Cryoprotection (reservoir + 20% glycerol), sitting drop vapor ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2012 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2.65→275.36 Å / Num. all: 43996 / Num. obs: 43996 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / R_merge(I) obs: 0.095 / R_sym value: 0.095 / Net I/σ(I): 23.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.65-2.79	15.3	0.869	0.9	96889	6328	0.869	98.2
2.79-2.96	15.3	0.555	1.4	91364	5976	0.555	98.2
2.96-3.17	15.2	0.296	2.6	86219	5655	0.296	98.3
3.17-3.42	15.2	0.187	4.1	80337	5277	0.187	98.6
3.42-3.75	15.1	0.104	7.2	73954	4885	0.104	98.7
3.75-4.19	15.1	0.071	10.3	66732	4433	0.071	98.8
4.19-4.84	14.8	0.055	12.2	58510	3947	0.055	99
4.84-5.93	14.5	0.052	12.8	48826	3360	0.052	99.1
5.93-8.38	14.2	0.044	13.7	37691	2660	0.044	99.1
8.38-92.47	12.8	0.035	17.2	18847	1475	0.035	94.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BBY

3bby

Resolution: 2.65→92.47 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7727 / SU ML: 0.27 / σ(F): 0 / σ(I): 0 / Phase error: 28.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2543	2228	5.08 %	RANDOM
R_work	0.1981	-	-	-
all	0.201	43896	-	-
obs	0.201	43896	97.94 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 208.67 Å² / B_iso mean: 61.9006 Å² / B_iso min: 19.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→92.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7209	0	100	86	7395

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7462
X-RAY DIFFRACTION	f_angle_d	1.074	10136
X-RAY DIFFRACTION	f_chiral_restr	0.067	1132
X-RAY DIFFRACTION	f_plane_restr	0.005	1312
X-RAY DIFFRACTION	f_dihedral_angle_d	16.117	2758

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.65-2.7076	0.326	128	0.261	2553	2681	98
2.7076-2.7706	0.3342	143	0.245	2566	2709	98
2.7706-2.8399	0.258	123	0.2312	2578	2701	97
2.8399-2.9167	0.2814	132	0.2253	2568	2700	98
2.9167-3.0025	0.3283	126	0.2257	2597	2723	98
3.0025-3.0994	0.3007	146	0.2085	2566	2712	97
3.0994-3.2101	0.2658	133	0.2078	2525	2658	98
3.2101-3.3386	0.2714	141	0.2113	2602	2743	98
3.3386-3.4905	0.3221	156	0.1932	2611	2767	98
3.4905-3.6744	0.2352	135	0.178	2575	2710	98
3.6744-3.9045	0.24	151	0.1746	2598	2749	98
3.9045-4.2058	0.2113	145	0.1705	2602	2747	98
4.2058-4.6287	0.2187	154	0.1602	2652	2806	99
4.6287-5.2977	0.2232	133	0.1805	2640	2773	99
5.2977-6.6713	0.2415	129	0.2138	2706	2835	99
6.6713-46.235	0.2653	153	0.2257	2729	2882	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	3.1123	-0.2848	0.2387	2.2364	-1.632	5.2137	-0.0482	-0.0265	0.3899	0.1528	-0.3774	-0.4125	-0.8318	0.8051	0.348	0.4436	-0.1524	0.0137	0.4009	0.071	0.2957	-19.2896	-7.5806	13.3983
2	3.4154	-1.7061	0.1851	6.4865	-0.6763	6.7266	0.1121	0.0294	-0.2895	-0.1687	0.0939	0.4228	0.7933	-0.5254	-0.0873	0.3918	-0.073	0.0026	0.3123	-0.0002	0.1949	-33.2633	-21.0057	5.0151
3	4.9351	0.0579	0.8683	2.2895	1.0032	5.6458	-0.0966	0.4088	0.1097	-0.2011	0.027	-0.2469	-0.0124	0.6605	0.1266	0.245	0.011	0.0671	0.3734	0.0696	0.1595	-23.1029	-17.5684	-3.4867
4	3.7391	-1.152	0.8395	0.6604	-1.2132	3.1625	0.2009	0.2497	-0.7674	0.1222	0.2409	-1.8063	1.2986	0.3439	0.0225	0.8194	0.1965	0.047	0.4429	-0.351	1.427	-30.8785	-79.3916	24.4149
5	2.0285	-0.9553	1.6202	2.9637	-0.2496	1.3739	0.9586	0.6871	-0.8452	-0.1445	0.2574	-1.3605	1.0408	0.0294	-0.256	0.726	-0.0576	-0.1177	0.3498	-0.346	0.9899	-33.0352	-77.814	26.6735
6	4.6273	-0.1724	0.0622	1.8521	-0.1303	3.9195	-0.0779	-0.0324	0.0683	-0.0276	0.4423	-1.1252	-0.6961	0.4667	-0.1519	0.5955	-0.231	0.0768	0.381	-0.2173	0.6599	-34.0369	-62.6058	27.0517
7	6.6792	-2.0371	2.2657	4.1528	-1.3037	8.0483	-0.0352	-0.5952	0.1264	0.0232	0.1647	0.6171	-1.2039	-1.5451	0.2613	0.6719	-0.0821	-0.0485	0.6153	-0.2129	0.2773	-57.6408	-67.9207	23.1954
8	4.0155	0.0898	0.1644	3.5172	4.6607	6.4699	-0.4639	0.6933	0.5973	-1.1934	0.2796	-0.6229	-1.2559	0.077	0.1262	1.2345	-0.3279	0.06	0.4332	-0.0192	0.5145	-43.4118	-57.7652	13.0018
9	7.3353	6.0394	5.61	5.8354	5.2486	4.904	1.0708	0.6355	-1.1808	0.3299	0.1309	-0.8767	0.1714	0.1389	-0.8956	0.688	-0.1041	0.0079	0.4238	-0.1017	0.3937	-48.4608	-69.7262	17.8505
10	5.8678	3.8262	0.3544	5.0338	-1.1588	1.0148	0.1012	-0.1412	-0.2991	-0.7067	0.0027	0.2878	-1.4608	0.2202	-0.1232	0.9423	-0.0551	0.1133	0.3856	-0.1326	0.3487	-51.4729	-66.5335	10.1455
11	6.2608	2.6706	3.5283	3.4202	-1.8331	8.0258	0.834	0.8358	-0.9448	-0.3215	0.3211	-1.0352	-0.3139	0.7775	-0.7434	0.7128	-0.0665	0.3912	0.5882	-0.361	0.8972	-35.0859	-77.5494	12.188
12	4.3666	1.4657	1.2156	5.8604	3.6166	5.4311	0.3276	-0.2631	0.1288	0.3133	-0.5678	0.0214	-0.0997	-1.0148	0.3282	0.7357	-0.1573	-0.0123	0.3642	-0.0883	0.2882	-46.3178	-56.0693	37.9979
13	1.6262	1.4631	0.5612	4.8183	0.668	2.0156	0.8287	-0.996	-0.2524	1.002	-0.5318	-0.419	0.9564	-0.823	-0.1207	1.4403	-0.5379	-0.1816	0.59	0.1648	0.4888	-43.3631	-69.0484	49.9097
14	5.6733	-1.3699	4.3054	0.5116	-0.5288	4.8422	0.814	0.329	-0.6844	-0.701	-0.0354	0.1807	1.0678	-1.2306	0.3031	0.5517	-0.1269	0.054	1.4044	0.4201	0.1915	-47.4985	-24.4429	23.4968
15	2.4641	0.8624	-0.0318	1.8615	-0.6338	3.2067	-0.4341	-0.6216	0.0933	-0.5191	-0.0097	0.3815	0.5122	-2.2353	-0.0353	0.2204	-0.2059	0.126	1.0141	0.1776	0.3025	-44.147	-20.2582	20.4788
16	8.1404	-1.5867	-0.1416	3.2098	1.1779	4.9402	-0.1031	-0.0762	0.4099	0.3924	0.0537	0.156	-0.8314	-0.4565	0.013	0.5063	0.0528	0.0669	0.2609	0.057	0.1762	-31.64	-11.6622	24.7097
17	5.1025	-0.3978	-0.8132	4.7505	6.2947	2.0405	-0.35	-0.1076	0.1471	0.0319	0.3542	-0.7118	0.2745	1.7208	-0.2329	0.4403	-0.1568	-0.0225	0.4581	0.1444	0.3319	-16.9962	-23.0523	30.6568
18	9.0875	-2.6158	3.8907	1.9168	-2.9324	4.6412	-0.1575	-1.1906	0.9099	0.7625	0.1759	0.1508	-1.9425	-0.5573	0.1289	0.8854	0.005	0.0512	0.264	-0.0452	0.3273	-29.1653	-9.4579	37.3097
19	4.9569	-6.1193	4.9269	7.4894	-5.9098	4.9913	0.2833	-0.5296	-0.4279	-0.1189	0.09	0.8838	0.7511	-1.053	-0.3835	0.44	-0.0794	0.1014	0.3429	-0.0675	0.2891	-29.6835	-21.0913	32.0435
20	4.118	-4.0818	0.3517	6.4531	0.0586	3.3398	0.0535	0.1135	-0.1867	0.3953	-0.2778	-0.2233	-0.1442	-0.0992	0.2637	0.4666	-0.1359	0.0306	0.2738	0.0116	0.1858	-26.1345	-21.4457	40.4148
21	5.0551	4.4058	0.9877	3.9166	0.8066	4.4938	0.1973	0.2128	0.2303	0.9567	0.0321	0.9806	0.2552	-0.5153	-0.4767	0.4637	0.0247	0.1059	1.0404	0.1567	0.4272	-45.7901	-24.9899	35.8118
22	2.4846	-0.4906	0.3829	3.1485	0.7066	5.1379	-0.2002	-0.2593	-0.0074	-0.006	0.1162	0.5083	0.5407	-0.9122	0.1186	0.2899	-0.1876	-0.0457	0.4073	-0.0423	0.333	-41.291	-40.3403	63.8501
23	3.7187	0.9776	0.0713	5.4769	-2.0201	5.3394	-0.0437	0.0917	0.0431	0.1172	-0.1391	-0.4365	0.3622	0.7915	0.0982	0.2428	0.0356	-0.0495	0.2208	0.0294	0.219	-21.3251	-35.0677	57.3502
24	5.2664	5.9692	-4.9211	9.3954	-7.1743	6.2388	-0.055	0.2909	0.2533	0.2076	0.3745	0.3795	-0.8264	-0.6682	-0.1901	0.4096	-0.0168	-0.0722	0.2603	-0.0559	0.157	-27.8875	-31.0816	53.8442
25	6.7777	4.7187	-0.6527	6.9961	-1.7155	3.3818	-0.2295	0.9584	0.7827	0.2748	0.0142	0.6856	0.4779	0.2501	0.1784	0.3681	0.0663	-0.0197	0.2814	-0.0114	0.2358	-23.972	-31.2205	45.9069
26	7.164	-2.6999	-0.931	5.802	-0.6157	3.866	-0.0508	0.1099	-0.6357	-0.9194	0.1396	0.8265	0.2329	-1.7261	-0.2014	0.4478	-0.1098	-0.1648	0.6914	-0.036	0.3597	-42.9255	-35.3584	49.1245

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 95 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 96 through 180 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 181 through 212 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 16 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 17 through 64 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 65 through 109 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 110 through 152 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 153 through 165 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 166 through 180 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 181 through 197 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 198 through 212 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 3 through 111 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 112 through 212 )	C
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 4 through 16 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 17 through 82 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 83 through 135 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 136 through 152 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 153 through 165 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 166 through 178 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 179 through 198 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 199 through 213 )	D
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 4 through 95 )	E
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 96 through 165 )	E
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 166 through 180 )	E
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 181 through 197 )	E
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 198 through 212 )	E

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