PDB-4zb9: Crystal structure of the glutathione transferase URE2P8 from Phan...

ID or keywords:

Entry

Database: PDB / ID: 4zb9

Title

Crystal structure of the glutathione transferase URE2P8 from Phanerochaete chrysosporium, with one glutathione disulfide bound per dimer.

Components

PcUre2p8

Keywords

TRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD / OXIDIZED GLUTATHIONE

Function / homology

Function and homology information

glutathione transferase
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.403 Å

Authors

Roret, T. / Didierjean, C.

Citation

Journal: Fungal Genet. Biol. / Year: 2015
Title: Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungi.
Authors: Roret, T. / Thuillier, A. / Favier, F. / Gelhaye, E. / Didierjean, C. / Morel-Rouhier, M.

History

Deposition	Apr 14, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zb9.cif.gz	372.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zb9.ent.gz	308.8 KB	Display	PDB format
PDBx/mmJSON format	4zb9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zb9_validation.pdf.gz	990.5 KB	Display	wwPDB validaton report
Full document	4zb9_full_validation.pdf.gz	1003 KB	Display
Data in XML	4zb9_validation.xml.gz	34.4 KB	Display
Data in CIF	4zb9_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/4zb9 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zb9	HTTPS FTP

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Related structure data

Related structure data	4f0cC 4zb6C 4zb7C 4zb8C 4zbaSC 4zbbC 4zbdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4e8h-1 7db4-d 4zbb-2 3zmk-2 6keo-d 4pnf-3 6kel-d 4zbb-1 4zba-2 6keq-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) 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 (9)

Deposited unit

A: PcUre2p8

B: PcUre2p8

C: PcUre2p8

D: PcUre2p8

hetero molecules

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

1

A: PcUre2p8

B: PcUre2p8

hetero molecules

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

2

C: PcUre2p8

D: PcUre2p8

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.913, 88.913, 240.426
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	PcUre2p8 Mass: 26204.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4I985*PLUS
#2: Chemical	ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₃₂N₆O₁₂S₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.73 %
Crystal grow	Temperature: 278 K / Method: microbatch Details: 30 % PEG4000, 0.1M TRIS pH8.5, 0.2M Sodium Acetate trihydrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.999 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2.4→44.5 Å / Num. obs: 38501 / % possible obs: 99.6 % / Redundancy: 13.2 % / R_merge(I) obs: 0.086 / Net I/σ(I): 23.3
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 12.8 % / R_merge(I) obs: 0.355 / Mean I/σ(I) obs: 7.6 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZBA

4zba

Resolution: 2.403→44.456 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2726	1921	5.01 %
R_work	0.2163	-	-
obs	0.2191	38366	99.54 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.679 Å² / k_sol: 0.378 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.8436 Å²	-0 Å²	0 Å²
2-	-	-5.8436 Å²	-0 Å²
3-	-	-	11.6872 Å²

Refinement step

Cycle: LAST / Resolution: 2.403→44.456 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7272	0	81	187	7540

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7570
X-RAY DIFFRACTION	f_angle_d	1.129	10248
X-RAY DIFFRACTION	f_dihedral_angle_d	17.429	2742
X-RAY DIFFRACTION	f_chiral_restr	0.078	1056
X-RAY DIFFRACTION	f_plane_restr	0.005	1304

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 (%)
2.4032-2.4633	0.3044	123	0.2404	2433	X-RAY DIFFRACTION	95
2.4633-2.5299	0.3046	129	0.2374	2568	X-RAY DIFFRACTION	100
2.5299-2.6044	0.3271	128	0.2433	2566	X-RAY DIFFRACTION	100
2.6044-2.6884	0.3093	128	0.2535	2584	X-RAY DIFFRACTION	100
2.6884-2.7845	0.3255	128	0.2387	2589	X-RAY DIFFRACTION	100
2.7845-2.8959	0.3164	138	0.2376	2547	X-RAY DIFFRACTION	100
2.8959-3.0277	0.2982	140	0.2446	2588	X-RAY DIFFRACTION	100
3.0277-3.1873	0.3162	113	0.2383	2621	X-RAY DIFFRACTION	100
3.1873-3.3869	0.2826	165	0.2374	2568	X-RAY DIFFRACTION	100
3.3869-3.6483	0.2743	144	0.218	2579	X-RAY DIFFRACTION	100
3.6483-4.0153	0.2436	157	0.2055	2604	X-RAY DIFFRACTION	99
4.0153-4.5958	0.2224	140	0.1691	2645	X-RAY DIFFRACTION	100
4.5958-5.7882	0.2374	151	0.1866	2684	X-RAY DIFFRACTION	100
5.7882-44.4641	0.2623	137	0.2114	2869	X-RAY DIFFRACTION	100

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	1.4218	-0.6411	-0.0302	0.9701	0.2973	0.4998	-0.1531	-0.7339	0.5094	0.2273	0.3424	-0.2579	-0.2413	0.3424	0.2686	1.0401	-0.2372	0.1982	0.5535	-0.3842	-0.0001	9.5108	15.3494	37.1396
2	2.173	1.1307	0.5203	1.2633	0.5202	1.3267	0.2146	-0.4724	0.7155	0.6556	-0.0855	-0.3933	-0.4523	0.2114	-0.0488	0.9013	-0.1425	-0.104	0.1454	-0.1004	0.4383	10.391	10.329	34.09
3	2.6604	-1.0842	0.1124	1.2631	0.3661	2.7853	-0.1539	-0.3653	0.4519	0.9015	0.1922	0.4819	-0.5971	-0.2638	-0.0081	0.6832	-0.0136	0.168	0.3241	-0.0021	0.5104	-3.2961	8.1801	41.209
4	4.1244	0.0382	-2.2003	2.4994	-0.4577	3.2312	-0.2096	-0.4223	-0.4646	0.15	0.057	0.0138	-0.4803	0.2686	0.0155	0.2893	-0.0402	-0.0116	0.1833	0.0822	0.214	2.2487	1.5983	21.3197
5	1.972	-0.5667	0.4946	1.4047	-0.0522	1.189	-0.2185	-0.0648	0.5923	0.0304	0.2092	0.6134	-0.2833	-0.1477	-0.017	0.3589	0.0687	0.0349	0.1796	0.0765	0.5214	-5.9382	6.8839	18.7849
6	2.0606	0.4093	-0.6079	0.4797	-0.9814	2.0297	0.242	0.0885	0.6513	0.1522	0.2361	0.3107	-0.1805	-0.0768	-0.2251	0.4616	0.0778	0.0154	0.2315	0.0204	0.5759	-7.514	14.8102	15.1237
7	5.8663	0.8751	-1.1525	0.3631	0.5137	3.603	-0.039	0.0998	0.696	0.3019	-0.287	-0.3914	-1.1166	0.1154	-0.0082	0.8513	-0.0952	-0.0428	0.2341	-0.0597	0.7308	4.5072	22.1664	25.8962
8	1.6351	-0.5932	0.4431	0.6104	0.9403	4.0783	0.2028	-0.1596	-0.1864	-0.0445	-0.0075	0.3396	0.037	-1.0597	-0.2066	0.1823	-0.0203	-0.0087	0.3577	0.1813	0.5856	-12.4431	-17.859	28.939
9	1.5015	2.059	-0.0073	3.0185	-0.0601	4.6309	0.3885	-0.4638	-0.49	-0.0302	0.288	0.4779	-0.1848	-0.6162	-0.3809	0.1752	0.0745	0.099	0.3354	0.185	0.5948	-16.148	-8.1895	23.5081
10	2.5325	-0.1495	-0.8233	1.5783	0.7625	2.8302	0.0685	-0.1838	0.0628	0.3701	-0.0112	0.0224	-0.0695	-0.1265	0.0339	0.2841	0.0005	-0.0226	0.1546	0.0657	0.3121	3.265	-7.925	30.6082
11	3.9027	0.0778	-1.5469	1.6861	-1.3156	5.3548	0.2542	-0.24	-0.0456	0.3643	-0.0325	-0.1044	-0.0304	-0.2429	-0.4299	0.2938	0.0228	-0.0358	0.1829	0.0579	0.2161	5.1107	-14.234	36.1159
12	2.9178	0.6456	-0.5486	1.0257	-1.7689	4.0449	-0.1306	-0.0501	-0.3327	0.1906	-0.1907	-0.5685	0.1011	0.0799	-0.3373	0.2856	0.0926	-0.1773	0.3237	0.1234	0.498	11.5919	-20.4495	34.1214
13	2.1862	0.4598	0.1447	6.521	5.0218	4.8739	-0.2599	0.1858	0.2953	0.5076	0.246	0.5906	1.1709	0.141	-0.0439	0.3702	0.0655	0.0625	0.2525	0.1412	0.6126	-4.3762	-26.271	29.2856
14	2.5388	0.0155	0.1727	2.576	1.3269	1.6631	-0.1512	-0.309	0.1479	-0.1307	-0.0934	0.5049	0.0461	-0.2698	0.0566	0.2922	0.0222	-0.064	0.2106	0.092	0.6378	-9.762	-30.6256	0.8771
15	1.0067	-0.4945	0.2532	1.7618	0.8189	2.0566	-0.0836	0.0459	0.3343	-0.1163	0.033	-0.0832	-0.3806	0.0278	-0.0059	0.311	-0.0258	-0.0514	0.1562	0.059	0.3271	9.2983	-31.3633	1.9097
16	2.3646	0.5929	2.0242	1.8758	0.228	6.0382	0.0613	0.5145	-0.5392	-0.3159	0.2041	-0.568	0.5514	0.0515	-0.0731	0.3836	0.0076	0.0497	0.2441	-0.0826	0.3671	15.5388	-59.8871	-1.6969
17	2.7377	1.2081	0.9402	3.2077	0.6936	2.276	-0.0779	0.3006	-0.7468	0.2578	0.3277	-0.6444	0.264	0.2384	-0.1865	0.2778	0.0644	-0.0157	0.1441	-0.0056	0.3266	15.239	-54.9942	1.5828
18	3.7649	0.5583	-0.0988	0.8237	0.4112	1.5976	-0.0626	0.3498	-0.6422	-0.4326	0.0703	0.2012	-0.0201	0.2247	0.031	0.4623	-0.0096	-0.0261	0.1134	0.0165	0.3472	6.1243	-52.6375	-9.7199
19	1.5527	-0.2879	1.5911	1.4304	0.1802	3.7121	0.0051	0.0391	0.2861	0.0315	-0.0985	0.0597	0.1895	0.1148	0.0558	0.3281	0.0183	0.015	0.1598	0.0758	0.3383	2.761	-46.1178	9.9044
20	4.075	4.0588	5.4417	5.2025	5.0053	7.9069	-0.0735	-0.6831	0.2386	0.9551	-0.1854	0.447	0.2161	-0.6793	0.2069	0.3964	0.1386	0.159	0.2418	0.0169	0.4148	-4.9729	-46.1329	16.7734
21	5.097	-0.2552	-3.65	1.2475	-0.1153	3.0386	-0.4108	0.3852	-0.4641	0.2461	0.175	0.9032	0.4045	-0.5605	0.1994	0.2774	-0.0334	-0.0299	0.2903	0.077	0.7534	-12.5625	-54.663	-0.7709
22	2.1676	0.4565	1.426	1.6344	2.0777	4.1492	-0.0792	-0.1139	-0.5506	0.3559	0.014	0.0336	0.6665	-0.0996	-0.0081	0.3042	0.0073	0.0568	0.2177	0.096	0.4759	0.1601	-55.5356	9.769
23	4.1081	0.4578	2.1186	2.0375	0.2176	1.0992	0.5259	-0.8021	-0.4526	-0.009	0.0704	-0.0642	0.4853	-0.3429	-0.0077	0.3212	-0.0477	0.0042	0.1978	0.093	0.5885	-7.9741	-59.2385	13.004
24	8.2256	1.2898	4.8467	2.421	2.6537	9.2703	0.274	-0.3663	-0.9147	0.0586	-0.1164	-0.2851	1.21	0.0733	-0.3136	0.3357	-0.0113	0.0379	0.2455	0.0578	0.3154	6.9636	-66.8303	6.7291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:17)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 18:60)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 61:100)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 101:133)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 134:183)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 184:206)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 207:221)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 3:42)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 43:74)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 75:155)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 156:183)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 184:206)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 207:221)
14	X-RAY DIFFRACTION	14	chain 'I' and (resseq 3:74)
15	X-RAY DIFFRACTION	15	chain 'I' and (resseq 75:221)
16	X-RAY DIFFRACTION	16	chain 'M' and (resseq 3:17)
17	X-RAY DIFFRACTION	17	chain 'M' and (resseq 18:60)
18	X-RAY DIFFRACTION	18	chain 'M' and (resseq 61:98)
19	X-RAY DIFFRACTION	19	chain 'M' and (resseq 99:133)
20	X-RAY DIFFRACTION	20	chain 'M' and (resseq 134:155)
21	X-RAY DIFFRACTION	21	chain 'M' and (resseq 156:167)
22	X-RAY DIFFRACTION	22	chain 'M' and (resseq 168:183)
23	X-RAY DIFFRACTION	23	chain 'M' and (resseq 184:206)
24	X-RAY DIFFRACTION	24	chain 'M' and (resseq 207:221)

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