PDB-4q5r: Crystal Structure of Glutathione S-transferase Bla g 5

ID or keywords:

Entry

Database: PDB / ID: 4q5r

Title

Crystal Structure of Glutathione S-transferase Bla g 5

Components

Glutathione S-transferase

Keywords

TRANSFERASE

Function / homology

Function and homology information

glutathione transferase /

glutathione transferase activity
Similarity search - Function

Biological species

Blattella germanica (German cockroach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.249 Å

Authors

Pedersen, L.C. / Mueller, G.A.

Citation

Journal: To be Published
Title: Crystal Structure of Glutathione S-transferase Bla g 5
Authors: Pedersen, L.C. / Mueller, G.A.

History

Deposition	Apr 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4q5r.cif.gz	486.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4q5r.ent.gz	419.7 KB	Display	PDB format
PDBx/mmJSON format	4q5r.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/q5/4q5r ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5r	HTTPS FTP

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Related structure data

Related structure data	4q5f 4q5n 4q5q
Similar structure data	4iel-1 2pmt-2 4gci-d 2vcq-2 1f2e-1 4pnf-2 5uas-2 4mk3-1 2pmt-1 1f2e-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

Related structure data

4q5f

4q5n

4q5q

Similar structure data

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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

C: Glutathione S-transferase

D: Glutathione S-transferase

B: Glutathione S-transferase

F: Glutathione S-transferase

E: Glutathione S-transferase

hetero molecules

145 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutathione S-transferase

B: Glutathione S-transferase

hetero molecules

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

2

C: Glutathione S-transferase

D: Glutathione S-transferase

hetero molecules

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

3

F: Glutathione S-transferase

E: Glutathione S-transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.063, 102.379, 165.765
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glutathione S-transferase / / GST class-sigma / Major allergen Bla g 5 Mass: 23364.686 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blattella germanica (German cockroach) / Production host: Escherichia coli (E. coli) / References: UniProt: O18598, glutathione transferase
#2: Chemical	ChemComp-GSH / GLUTATHIONE / Glutathione Mass: 307.323 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris, PEG4000, glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2012
Radiation	Monochromator: si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.249→50 Å / Num. all: 58152 / Num. obs: 58152 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / B_iso Wilson estimate: 36.62 Å² / R_sym value: 0.109 / Net I/σ(I): 8
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 2541 / R_sym value: 0.456 / % possible all: 86.4

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Processing

Software

Name	Version	Classification
SERGUI		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.249→48.625 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.245	2337	4.03 %	random
R_work	0.2049	-	-	-
all	0.21	58043	-	-
obs	0.2065	58015	98.23 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.249→48.625 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9358	0	178	480	10016

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9801
X-RAY DIFFRACTION	f_angle_d	0.766	13311
X-RAY DIFFRACTION	f_dihedral_angle_d	13.085	3608
X-RAY DIFFRACTION	f_chiral_restr	0.042	1396
X-RAY DIFFRACTION	f_plane_restr	0.004	1705

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2492-2.2951	0.3212	114	0.27	2766	X-RAY DIFFRACTION	84
2.2951-2.345	0.329	125	0.2619	3051	X-RAY DIFFRACTION	93
2.345-2.3995	0.3	134	0.2517	3178	X-RAY DIFFRACTION	96
2.3995-2.4595	0.3132	132	0.2554	3240	X-RAY DIFFRACTION	98
2.4595-2.526	0.2857	142	0.2501	3290	X-RAY DIFFRACTION	100
2.526-2.6004	0.2785	141	0.2348	3292	X-RAY DIFFRACTION	100
2.6004-2.6843	0.2996	135	0.2327	3285	X-RAY DIFFRACTION	100
2.6843-2.7802	0.281	140	0.2338	3321	X-RAY DIFFRACTION	100
2.7802-2.8915	0.3109	138	0.2371	3285	X-RAY DIFFRACTION	100
2.8915-3.0231	0.2695	143	0.2441	3300	X-RAY DIFFRACTION	100
3.0231-3.1825	0.2338	134	0.2317	3322	X-RAY DIFFRACTION	100
3.1825-3.3818	0.27	144	0.2194	3329	X-RAY DIFFRACTION	100
3.3818-3.6428	0.2504	141	0.194	3341	X-RAY DIFFRACTION	100
3.6428-4.0093	0.195	139	0.1817	3366	X-RAY DIFFRACTION	100
4.0093-4.589	0.1821	143	0.1606	3357	X-RAY DIFFRACTION	100
4.589-5.7802	0.2254	144	0.1786	3419	X-RAY DIFFRACTION	100
5.7802-48.6364	0.2273	148	0.1813	3536	X-RAY DIFFRACTION	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	3.0217	-0.0829	0.8641	0.7375	-0.8022	1.6991	0.0069	-0.4525	-0.2007	0.4989	0.1749	-0.0507	-0.0453	0.3887	-0.0991	0.3621	0.0901	0.0917	0.4714	0.0635	0.2899	34.3073	33.6914	55.1965
2	1.0781	-0.0075	-0.0484	0.7074	-0.3331	2.2613	0.1737	-0.3313	-0.0789	0.3765	-0.0831	0.0714	-0.2972	0.1596	-0.1132	0.7035	0.0291	0.1309	0.7437	0.2882	0.3619	36.6958	31.4823	60.3893
3	1.6774	0.3799	0.3061	1.0409	-0.4117	0.2963	0.1003	-0.3786	0.017	0.6379	-0.3044	-0.537	-0.2595	0.619	0.0477	0.514	-0.0202	-0.1815	0.8151	0.0729	0.4583	47.7682	42.2475	55.3426
4	1.4647	-0.328	0.8355	1.2961	-1.5784	2.5881	-0.3976	-0.3492	-0.0488	0.1227	0.2834	-0.1177	0.4821	0.487	-0.0018	0.3533	0.1166	0.0009	0.5143	0.1252	0.346	44.4663	30.3853	51.347
5	0.291	-0.1526	-0.0877	0.7345	-0.4378	0.4993	-0.1489	-0.0924	-0.4382	-0.1196	-0.1157	0.1157	0.555	0.1687	-0.2734	0.3259	0.1051	0.1238	0.0545	0.1896	0.5306	32.9696	27.0239	42.7118
6	1.577	-0.4071	-0.4658	2.1611	0.8328	2.3054	0.0058	0.0155	0.0806	-0.4107	-0.0548	0.4647	-0.3256	0.008	-0.0339	0.2523	-0.0058	0.0063	0.2129	-0.0022	0.2883	30.116	41.2173	38.4803
7	1.4394	-0.593	-0.4432	1.3355	0.0062	1.4589	0.2161	0.2078	0.0918	-0.0481	-0.1422	0.3862	-0.3647	-0.2404	-0.0597	0.3366	0.0206	0.0697	0.1868	0.0103	0.4317	23.6252	48.8471	40.9866
8	1.334	-0.5932	-0.6289	1.5287	-0.2657	0.7899	-0.1285	-0.4445	-0.1179	0.0744	0.2667	0.4184	-0.1128	0.2244	-0.1162	0.275	0.0068	0.0961	0.1828	0.0527	0.2904	26.6689	41.5497	48.6404
9	1.3621	-0.0045	0.0817	1.6334	-0.2103	1.114	-0.0038	-0.1181	-0.2719	0.0025	-0.039	0.6861	-0.1152	-0.2054	0.0475	0.3334	0.0641	0.1428	0.2753	0.0367	0.6109	16.598	42.0845	48.0099
10	1.3321	1.3542	0.3783	4.2822	0.3443	1.7506	-0.1983	-0.7996	-0.2468	0.5467	0.215	0.5933	-0.5346	-0.0529	0.0136	0.5868	0.1304	0.2299	0.5205	0.1454	0.5317	25.1375	35.6091	60.0662
11	2.4922	-0.6469	0.6783	0.4279	-0.4515	1.5989	0.3698	0.773	-0.0988	-0.4664	-0.2093	-0.055	0.1327	0.3184	-0.1537	0.3726	0.1482	0.0205	0.8469	-0.0412	0.2851	76.113	17.7625	50.8523
12	1.7561	0.2599	0.1713	0.9436	0.2778	2.2193	0.1648	0.5777	0.0343	-0.1832	-0.1907	0.1772	0.0786	-0.6329	0.0225	0.2534	0.0547	-0.0199	0.6017	-0.0274	0.2547	60.3902	18.9041	61.6228
13	4.0801	-0.358	-0.9963	1.0933	0.3398	2.9595	0.2775	-0.6036	0.0813	0.2859	0.0046	0.0917	0.1396	-0.0854	-0.2012	0.2497	-0.0294	-0.0072	0.3074	-0.0213	0.1981	72.0815	22.3139	87.2441
14	3.0997	0.3756	-0.8213	1.6368	1.105	1.3157	0.1587	-0.1649	-0.4393	0.4276	-0.2194	0.1765	0.4647	-0.3032	0.0146	0.3027	-0.1103	0.0058	0.3961	0.0426	0.3336	58.6673	15.9399	83.9898
15	0.9579	-0.4223	-0.0062	4.1551	2.5108	2.3486	0.0755	0.206	0.3238	0.1233	-0.0109	0.3357	-0.2	-0.2932	-0.0954	0.1743	-0.0167	0.0531	0.2893	-0.0258	0.254	64.3278	27.3646	81.4942
16	1.916	-0.2934	-0.4609	1.2907	0.1168	1.4191	0.1095	0.3746	-0.2412	-0.0284	-0.0576	-0.0359	0.1214	-0.0418	-0.0621	0.2105	0.0383	-0.0301	0.2948	-0.0744	0.2618	77.1997	13.8519	70.998
17	1.1063	-0.329	0.3103	1.3585	0.2825	1.4761	0.1359	0.0859	-0.1387	0.0617	-0.0305	-0.2905	0.2677	0.4685	-0.107	0.2333	0.0696	-0.0287	0.2898	-0.057	0.2631	87.0435	13.5083	74.5356
18	4.7604	0.6659	-0.6525	3.3645	0.0093	4.8649	0.3024	-0.4695	-0.3773	0.5146	-0.0301	-0.134	0.3798	-0.2403	-0.2865	0.3035	-0.0373	-0.0587	0.432	0.0022	0.2705	82.3969	18.1278	90.8148
19	2.0272	0.0539	-0.7339	0.7245	-0.1628	1.787	0.1637	0.5257	0.1854	-0.5672	-0.1014	0.0727	-0.0939	-0.446	-0.0191	0.4116	0.0331	-0.0056	0.3198	0.0354	0.241	35.3473	43.5257	20.9379
20	1.8484	0.2945	-1.1712	2.0109	-0.214	1.9315	0.0199	-0.2314	-0.0157	-0.2006	-0.1293	-0.4362	-0.07	0.3922	0.0851	0.2415	0.0247	0.0642	0.2852	0.0742	0.3402	47.3429	41.9053	32.8598
21	1.5218	-0.6689	-0.2477	1.4824	-0.4822	2.7557	-0.0962	-0.3028	-0.2284	0.6437	0.3397	-0.4182	0.3893	0.352	-0.1753	0.4956	0.1562	-0.0479	0.3593	-0.033	0.3689	87.499	55.5764	79.0933
22	1.6574	-0.965	-0.5564	1.3985	0.3049	1.5665	0.3818	0.0398	-0.0377	-0.112	-0.1659	0.1186	-0.0707	0.0775	-0.2223	0.4719	0.0169	0.0929	0.2595	-0.0406	0.3663	78.3851	61.8586	74.0386
23	0.2108	-0.1776	-0.0405	0.4395	0.3453	1.5308	0.1097	0.3175	-0.116	-0.242	-0.2199	0.3433	0.1474	-0.2352	0.1352	0.8043	0.3294	-0.0383	0.8477	-0.3842	0.6982	76.7882	51.4548	50.0334
24	0.5954	0.1885	-0.0957	0.8458	-0.0756	0.0305	0.6964	0.3324	0.4775	-1.0548	-0.1589	-0.685	-0.8112	0.0724	-0.2085	0.8034	0.1004	0.383	0.3705	0.0253	0.621	88.8741	65.5278	61.1741
25	2.2437	0.9652	0.4737	2.3471	0.0866	1.2372	-0.0027	-0.1033	0.2267	-0.2026	0.2112	-0.6174	0.3172	0.3089	-0.0881	0.4677	0.136	-0.0043	0.4598	-0.1555	0.7555	95.7674	54.8873	72.5045
26	0.7411	-0.1983	-0.4624	0.386	0.239	0.3813	0.4651	0.347	0.1782	-0.2943	-0.1362	0.1673	-0.2083	-0.0847	0.045	1.0929	0.7507	-0.1709	0.5205	-0.4238	0.6146	61.0826	76.7781	66.2261
27	0.2891	-0.0166	0.1767	0.4534	-0.1673	0.3384	0.1985	0.1911	0.0352	-0.2285	-0.187	0.2467	-0.0838	-0.0492	0.1072	1.1457	0.648	-0.013	0.699	-0.1915	0.5803	59.0673	82.7325	63.9441
28	0.4612	-0.148	0.0091	0.0489	-0.0045	-0.0008	0.0568	0.1617	0.0027	-0.2609	-0.1724	0.0695	-0.1762	-0.1216	-0.3862	1.6611	0.7658	0.0164	0.8681	0.0705	0.3562	71.0573	73.389	52.7962
29	2.3007	-0.2519	0.1299	1.5528	0.1514	1.645	0.5939	0.2162	-0.167	-0.6442	-0.4987	0.3296	-0.557	-0.3602	-0.172	0.5614	0.1337	0.0332	0.3008	-0.0856	0.348	69.152	69.5034	72.0177
30	0.7101	0.2688	0.4642	1.3699	0.9596	0.7955	0.3479	-0.1081	-0.0767	-0.0082	-0.0834	0.0298	-0.0081	-0.2526	-0.1682	0.649	0.1006	-0.2947	0.9052	-0.2063	1.2593	60.0304	46.6097	61.5743
31	0.7316	0.5719	-0.0024	2.172	1.4466	1.2184	0.2882	0.0011	-0.9517	0.0578	-0.9063	1.484	0.1963	-0.92	0.3878	0.5042	-0.0543	0.1005	0.5971	-0.3121	1.124	57.7978	62.3536	76.8678
32	0.1347	-0.12	-0.1223	0.1041	0.1092	0.1117	0.2428	0.2454	-0.0842	-0.289	-0.0541	0.0267	-0.0396	0.0414	0.0376	0.8128	0.3986	-0.1783	0.625	-0.5804	1.1339	50.5835	77.3877	68.3406

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 64 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 65 through 82 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 83 through 107 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 151 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 152 through 168 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 169 through 188 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 189 through 204 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 64 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 65 through 204 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 36 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 37 through 53 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 54 through 64 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 65 through 125 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 126 through 187 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 188 through 203 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 3 through 53 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 54 through 204 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 3 through 36 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 37 through 107 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 108 through 125 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 126 through 188 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 189 through 204 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 5 through 25 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 26 through 34 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 40 through 53 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 54 through 107 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 108 through 125 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 126 through 189 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 190 through 200 )

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