PDB-4ke3: Crystal structure of a glutathione transferase family member from...

ID or keywords:

Entry

Database: PDB / ID: 4ke3

Title

Crystal structure of a glutathione transferase family member from Burkholderia graminis, target efi-507264, no gsh, disordered domains, space group P21, form(2)

Components

Glutathione S-transferase domain

Keywords

TRANSFERASE / GST / glutathione S-transferase fold / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity
Similarity search - Function

Biological species

Burkholderia graminis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of a glutathione transferase family member from Burkholderia graminis, target efi-507264, no gsh, disordered domains, space group P21, form(2)
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ke3.cif.gz	464.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4ke3.ent.gz	388.8 KB	Display	PDB format
PDBx/mmJSON format	4ke3.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/ke/4ke3 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4ke3	HTTPS FTP

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Related structure data

Related structure data	4kdxS 4kdu S: Starting model for refinement
Similar structure data	4k6i-d 4kdx-2 4m8e-d 6lb6-d 4zsh-d 6jnr-1 1mv9-d 4kdu-2 4kdu-1 4poj-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) 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-507264

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (10) #255 - Mar 2021 Cisplatin and DNA similarity (8)

Deposited unit

A: Glutathione S-transferase domain

B: Glutathione S-transferase domain

C: Glutathione S-transferase domain

D: Glutathione S-transferase domain

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

1

A: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.211, 56.141, 98.299
Angle α, β, γ (deg.)	90.000, 91.350, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glutathione S-transferase domain Mass: 26086.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia graminis (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_2467 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1FZ96
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.07 Å³/Da / Density % sol: 40.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.15 M DL-Malic Acid, 20 %(w/v) PEG 3350); Cryoprotection (reservoir + 20% ethylene glycol), VAPOR DIFFUSION, ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.15 M DL-Malic Acid, 20 %(w/v) PEG 3350); Cryoprotection (reservoir + 20% ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 2.07 Å³/Da / Density % sol: 40.51 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.15 M DL-Malic Acid, 20 %(w/v) PEG 3350); Cryoprotection (reservoir + 20% ethylene glycol), VAPOR DIFFUSION, ...

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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: Apr 17, 2013 / 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: 1.9→100 Å / Num. all: 68251 / Num. obs: 68251 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.063 / R_sym value: 0.063 / Χ²: 0.92 / Net I/σ(I): 9.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.93	3.4	0.434	3388	1.168	1	99.4
1.93-1.97	3.4	0.434	3374	0.839	1	99.5
1.97-2.01	3.4	0.317	3341	0.796	1	99.5
2.01-2.05	3.5	0.266	3381	0.831	1	99.7
2.05-2.09	3.5	0.252	3420	1.062	1	99.8
2.09-2.14	3.5	0.2	3389	0.864	1	99.9
2.14-2.19	3.5	0.167	3383	0.824	1	99.9
2.19-2.25	3.6	0.165	3431	0.902	1	100
2.25-2.32	3.6	0.162	3387	1.086	1	99.9
2.32-2.39	3.6	0.108	3375	0.769	1	100
2.39-2.48	3.7	0.104	3422	0.761	1	100
2.48-2.58	3.7	0.087	3411	0.767	1	100
2.58-2.7	3.7	0.084	3408	0.899	1	100
2.7-2.84	3.8	0.082	3438	1.043	1	100
2.84-3.02	3.8	0.08	3385	1.31	1	100
3.02-3.25	3.8	0.075	3439	1.509	1	100
3.25-3.58	3.8	0.061	3455	1.267	1	100
3.58-4.09	3.8	0.038	3420	0.64	1	99.9
4.09-5.16	3.8	0.032	3486	0.434	1	100
5.16-100	3.7	0.043	3518	0.612	1	98.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data reduction
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KDX

4kdx

Resolution: 1.9→32.757 Å / Occupancy max: 1 / Occupancy min: 0.75 / FOM work R set: 0.8623 / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 20.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1988	2977	5.08 %	RANDOM
R_work	0.1527	-	-	-
all	0.155	58655	-	-
obs	0.155	58655	85.31 %	-

Solvent computation

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

Displacement parameters

B_iso max: 105.37 Å² / B_iso mean: 26.3923 Å² / B_iso min: 5.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→32.757 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6300	0	0	539	6839

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6460
X-RAY DIFFRACTION	f_angle_d	1.327	8790
X-RAY DIFFRACTION	f_chiral_restr	0.078	924
X-RAY DIFFRACTION	f_plane_restr	0.007	1150
X-RAY DIFFRACTION	f_dihedral_angle_d	12.397	2350

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8885-1.9195	0.286	80	0.2279	1394	1474	46
1.9195-1.9525	0.2573	93	0.1886	1676	1769	55
1.9525-1.988	0.2183	103	0.1675	1833	1936	59
1.988-2.0263	0.2291	98	0.1579	1944	2042	63
2.0263-2.0676	0.2452	123	0.1704	2079	2202	67
2.0676-2.1126	0.2049	117	0.167	2165	2282	71
2.1126-2.1617	0.206	122	0.165	2383	2505	76
2.1617-2.2158	0.2297	123	0.1645	2452	2575	80
2.2158-2.2757	0.314	141	0.2091	2691	2832	86
2.2757-2.3426	0.2244	148	0.1489	2827	2975	91
2.3426-2.4182	0.1993	142	0.1429	3014	3156	97
2.4182-2.5046	0.1807	183	0.1457	3041	3224	99
2.5046-2.6048	0.2046	162	0.145	3117	3279	100
2.6048-2.7233	0.2152	162	0.1426	3103	3265	100
2.7233-2.8668	0.197	190	0.153	3086	3276	100
2.8668-3.0463	0.2022	171	0.1584	3109	3280	100
3.0463-3.2813	0.2204	142	0.1581	3144	3286	100
3.2813-3.6112	0.1898	174	0.1537	3104	3278	100
3.6112-4.1328	0.1833	178	0.1304	3140	3318	100
4.1328-5.2036	0.1319	153	0.1217	3159	3312	100
5.2036-32.7622	0.2029	172	0.177	3217	3389	99

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	1.1916	0.4194	0.1744	0.9504	0.172	0.3584	-0.1282	0.3117	0.3313	-0.351	0.0205	0.4267	-0.0719	-0.1	0.016	0.1291	-0.0096	-0.0492	0.173	0.0142	0.1685	18.2012	-2.9247	-9.5466
2	1.0518	0.1875	0.1019	1.0916	0.0169	1.2135	0.0111	-0.1579	0.2563	0.2151	-0.0616	0.1243	-0.0474	-0.1214	0.0054	0.1024	-0.0218	0.0361	0.1153	-0.0605	0.1244	23.5417	1.785	9.0681
3	1.738	0.1297	-0.3382	0.5517	-0.0493	0.6641	0.0211	0.374	-0.1146	-0.2763	-0.0519	-0.4472	0.0555	0.2261	0.0183	0.1368	0.0074	0.0522	0.2018	0.006	0.2392	22.071	-15.0674	-58.7718
4	1.0697	0.0995	0.0157	1.0887	-0.0051	1.1664	-0.011	-0.221	-0.1559	0.1905	-0.034	-0.1739	0.0778	0.0861	0.0205	0.1026	-0.0189	-0.0239	0.1104	0.0443	0.104	16.7175	-19.7764	-40.0717
5	6.0526	-0.0796	0.6629	2.0545	0.0712	2.3566	-0.0492	-0.4257	0.0442	0.2222	-0.02	0.1352	-0.0871	-0.1704	-0.0122	0.4253	-0.0234	-0.086	0.2912	0.0226	0.1503	12.0801	6.8274	-30.9753
6	0.8487	-0.1794	0.5132	0.5008	-0.4225	0.9595	-0.0226	-0.0926	0.0051	0.1745	-0.0463	-0.2118	-0.13	0.0334	0.0023	0.1248	-0.0185	-0.0431	0.0752	0.034	0.1303	14.9459	8.1757	-40.3228
7	0.9502	0.069	0.2781	2.8946	-0.3885	1.1457	0.0057	-0.3721	-0.0096	0.2274	0.1116	-0.0839	-0.1692	-0.0118	-0.0343	0.219	-0.0038	-0.0136	0.1813	0.0382	0.125	7.1775	2.6369	-33.8057
8	0.7211	-0.1905	0.0491	0.9406	-0.2976	0.7493	0.0561	0.0326	0.0317	0.0022	0.0015	-0.0845	0.0316	-0.067	-0.0246	0.0705	-0.0089	-0.0054	0.0803	0.0163	0.1145	7.8129	2.8307	-47.5819
9	3.1686	0.0735	0.9617	1.4169	0.0564	1.3536	0.0466	0.2251	-0.0133	-0.2258	0.0572	-0.2534	-0.1592	0.1445	-0.0121	0.1343	-0.0078	0.0327	0.0861	0.0209	0.1595	18.1434	-2.2733	-53.2063
10	1.2672	0.1232	0.4859	1.1062	0.4309	1.3246	0.0269	-0.2158	-0.2385	0.3002	0.0437	-0.2434	0.1228	0.1508	-0.0546	0.1422	0.0327	-0.1587	0.1667	0.0829	0.414	32.0313	-2.0545	-37.9102
11	0.7309	-1.6703	0.1734	4.406	-0.7285	1.0208	-0.0498	-0.3704	0.0663	0.4695	0.1923	-0.0741	0.1247	0.1329	-0.0606	0.3531	-0.0038	-0.2419	0.4311	0.1203	0.517	36.8972	-0.3184	-28.1735
12	2.2618	-0.1722	1.1801	1.36	0.4074	2.2737	0.1647	0.0798	-0.2447	0.0517	0.1869	-0.6544	0.072	0.3312	0.2223	0.1135	0.0148	0.0535	0.19	-0.0053	0.4679	35.0324	0.481	-48.1954
13	0.937	0.0469	-0.4524	0.9969	0.2457	0.9468	0.0496	0.1578	0.15	-0.0932	-0.0292	-0.4751	-0.1985	-0.013	0.0087	0.0737	-0.0265	0.0007	0.0804	0.0533	0.2186	23.351	7.7467	-48.5485
14	0.0594	0.1377	0.0171	0.3226	-0.0226	0.3225	0.0166	0.0169	-0.0463	-0.1081	0.0511	-0.3211	-0.0681	0.1655	0.3139	0.1084	-0.0665	0.121	0.0951	0.084	0.4995	31.6807	12.0206	-48.7738
15	1.9181	-0.8924	1.7082	1.8212	-1.4811	3.1776	0.2359	-0.0281	0.0375	0.2751	-0.0352	-0.3549	0.0558	0.1985	0.0276	0.1396	-0.0295	-0.0406	0.0979	-0.0015	0.2354	21.2074	15.3602	-40.8688
16	8.3923	-0.4419	-1.2029	3.3218	0.2941	3.2499	-0.1176	-0.4413	0.0014	0.2299	-0.0128	-0.2525	0.1379	0.2739	0.0158	0.2793	-0.0417	0.0285	0.2574	0.0355	0.101	28.2264	-24.7972	18.0698
17	0.6648	-0.2331	-0.1464	0.6085	0.2487	1.0746	0.0102	-0.0602	-0.0747	0.0295	0.0222	0.0885	0.0795	-0.0604	0.0412	0.1067	-0.011	0.0326	0.1101	-0.0105	0.0537	25.3223	-26.15	8.8353
18	1.7311	-0.1963	-0.2767	2.5165	0.7067	1.1864	0.0013	-0.5584	-0.1274	0.3159	0.128	-0.1021	0.052	0.1016	-0.0439	0.1926	0.0158	-0.0125	0.2167	-0.0228	0.1144	33.0911	-20.5709	15.373
19	0.5478	-0.1905	0.1314	0.8068	0.2242	0.7537	0.0337	0.0657	-0.0495	0.0108	0.0151	-0.0779	-0.0396	0.0695	-0.0076	0.0748	0.0068	0.0113	0.0886	-0.0341	0.0691	32.4741	-20.7951	1.5571
20	2.7066	0.3213	-1.3588	1.2726	-0.4433	1.9267	0.038	-0.0206	0.3403	0.0112	0.0749	0.2376	0.0531	-0.0735	-0.0112	0.0802	-0.0076	-0.0099	0.0896	-0.0444	0.137	16.0534	-15.8081	2.6454
21	0.7854	-1.0809	-0.114	1.717	0.5555	0.6872	-0.1248	-0.3331	0.0034	0.2934	0.1674	0.1293	-0.1144	-0.2552	-0.0095	0.3806	0.005	0.1757	0.4607	-0.1157	0.2853	3.3151	-17.642	21.0785
22	2.4044	-0.2267	-1.851	1.449	-0.2903	3.5497	0.2092	-0.0145	0.2485	-0.0041	0.2131	0.4272	-0.1188	-0.2914	0.2539	0.1057	0.008	-0.0433	0.1971	-0.013	0.3236	5.2596	-18.4557	0.9062
23	1.0865	-0.171	-0.1211	1.4331	0.2291	0.6543	-0.001	0.1247	-0.1885	-0.0493	-0.0135	0.2314	0.1425	-0.0317	0.1404	0.1026	-0.0108	-0.0026	0.0998	-0.0395	0.0635	16.9427	-25.7456	0.5818
24	0.0354	0.0286	-0.1162	0.2881	0.0913	0.4998	0.0345	0.0924	-0.0458	-0.1001	-0.0052	0.2443	0.1047	-0.24	0.2587	0.0653	-0.0576	-0.1105	0.1225	-0.0939	0.3591	8.6336	-29.9969	0.3514
25	1.6624	-0.8363	-1.6976	2.2872	1.5794	3.317	0.1309	-0.0427	-0.198	0.2012	0.0106	0.071	0.0439	-0.1616	-0.0124	0.1105	-0.0285	-0.0068	0.1225	0.0263	0.2275	19.1136	-33.3487	8.2599

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 76 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 207 )	A
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 76 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 77 through 207 )	B
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 10 )	C
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 11 through 23 )	C
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 24 through 65 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 66 through 86 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 87 through 102 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 103 through 115 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 116 through 124 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 125 through 149 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 150 through 174 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 175 through 194 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 195 through 207 )	C
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 10 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 11 through 23 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 24 through 65 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 66 through 86 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 87 through 115 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 116 through 124 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 125 through 149 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 150 through 174 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 175 through 194 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 195 through 207 )	D

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