PDB-4zb7: Phanerochaete chrysosporium URE2P6 in apo form.

ID or keywords:

Entry

Database: PDB / ID: 4zb7

Title

Phanerochaete chrysosporium URE2P6 in apo form.

Components

PcUre2p6

Keywords

TRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD

Function / homology

Function and homology information

glutathione transferase
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 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	4zb7.cif.gz	282.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4zb7.ent.gz	231.5 KB	Display	PDB format
PDBx/mmJSON format	4zb7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zb7_validation.pdf.gz	480.3 KB	Display	wwPDB validaton report
Full document	4zb7_full_validation.pdf.gz	491.8 KB	Display
Data in XML	4zb7_validation.xml.gz	25.2 KB	Display
Data in CIF	4zb7_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/4zb7 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zb7	HTTPS FTP

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Related structure data

Related structure data	4f0cC 4zb6C 4zb8SC 4zb9C 4zbaC 4zbbC 4zbdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6sum-2 3wv5-2 5xky-d 6sum-1 5xkx-d 4rnv-4 6sun-d 4rnu-3 4rnu-2 1u5r-1 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: PcUre2p6

B: PcUre2p6

C: PcUre2p6

D: PcUre2p6

hetero molecules

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

1

A: PcUre2p6

B: PcUre2p6

hetero molecules

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

2

C: PcUre2p6

D: PcUre2p6

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.363, 84.888, 92.779
Angle α, β, γ (deg.)	90.00, 102.98, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PcUre2p6 Mass: 25567.875 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: A0A0R4I981*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.34 Å³/Da / Density % sol: 47.43 %
Crystal grow	Temperature: 278 K / Method: microbatch Details: 25 % PEG4000, 0.1M Sodium Acetate pH4.6, 0.2M Ammonium Sulfate

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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: Mar 27, 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→49.4 Å / Num. obs: 37186 / % possible obs: 99.9 % / Redundancy: 10.1 % / R_merge(I) obs: 0.08 / Net I/σ(I): 20.9
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 10.1 % / R_merge(I) obs: 0.674 / Mean I/σ(I) obs: 3.3 / % possible all: 99.1

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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: 4ZB8

4zb8

Resolution: 2.4→49.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2286	1853	4.99 %
R_work	0.1934	-	-
obs	0.1952	37135	99.78 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.91 Å² / k_sol: 0.348 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.455 Å²	0 Å²	-6.1217 Å²
2-	-	-15.1203 Å²	-0 Å²
3-	-	-	3.6653 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5229	0	31	97	5357

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5387
X-RAY DIFFRACTION	f_angle_d	1.246	7294
X-RAY DIFFRACTION	f_dihedral_angle_d	15.464	1927
X-RAY DIFFRACTION	f_chiral_restr	0.081	777
X-RAY DIFFRACTION	f_plane_restr	0.005	906

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 (%)
2.3956-2.4604	0.2838	138	0.2287	2646	X-RAY DIFFRACTION	98
2.4604-2.5328	0.3098	134	0.2316	2688	X-RAY DIFFRACTION	100
2.5328-2.6146	0.2672	147	0.2299	2730	X-RAY DIFFRACTION	100
2.6146-2.708	0.2707	129	0.2223	2718	X-RAY DIFFRACTION	100
2.708-2.8164	0.2785	171	0.2078	2665	X-RAY DIFFRACTION	100
2.8164-2.9446	0.2388	131	0.2063	2707	X-RAY DIFFRACTION	100
2.9446-3.0998	0.2745	144	0.2052	2720	X-RAY DIFFRACTION	100
3.0998-3.294	0.2355	143	0.2017	2732	X-RAY DIFFRACTION	100
3.294-3.5482	0.2195	154	0.1975	2681	X-RAY DIFFRACTION	100
3.5482-3.9052	0.221	142	0.1833	2732	X-RAY DIFFRACTION	100
3.9052-4.4699	0.1874	140	0.156	2734	X-RAY DIFFRACTION	100
4.4699-5.6304	0.206	140	0.1771	2744	X-RAY DIFFRACTION	100
5.6304-49.4236	0.2222	140	0.2044	2785	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	5.5443	0.3815	0.0134	2.6572	-0.2708	5.1879	-0.1735	-0.2961	0.5554	0.6756	-0.0227	-1.007	-0.6307	0.5998	0.0741	0.4895	-0.0936	-0.0335	0.3401	0.0051	0.5376	19.0896	8.6761	41.8749
2	6.3088	-0.9992	-0.8022	5.7408	5.3565	6.6	0.6121	-0.291	0.1277	0.1199	-0.4818	-0.8136	-0.6507	-0.1578	-0.0725	0.4701	-0.1669	-0.0117	0.2759	0.0473	0.4583	17.7151	12.025	41.6522
3	3.1687	1.6724	-1.5162	8.9378	-0.2335	4.4775	-0.1299	0.0788	0.1155	-0.3523	-0.0114	-0.1447	-0.1285	0.3366	0.1366	0.1783	-0.0232	-0.0237	0.2486	-0.0054	0.2599	11.0187	0.5495	34.9218
4	5.609	-0.214	-0.9715	5.2771	1.6972	6.7139	-0.512	-0.6503	-0.6068	1.1072	-0.3469	1.0195	-0.0877	-0.1753	0.3987	0.6499	0.1126	-0.058	0.3621	0.0638	0.5839	14.2625	-12.6437	54.1497
5	4.4269	-3.2548	1.0685	3.44	-3.9616	9.6081	0.2364	0.0981	0.0715	-1.3145	-0.377	-1.0114	1.0074	0.6827	0.0902	0.4392	0.1019	0.0397	0.3517	0.0253	0.578	18.9653	-15.4231	37.4871
6	6.6972	1.2191	-3.6371	9.4832	0.6958	5.0541	0.1847	-0.5702	-0.4609	0.8331	-0.4167	-0.5176	-0.2251	0.186	-0.0122	0.3272	-0.0171	-0.0608	0.2645	0.0635	0.422	19.3767	-5.0849	46.8345
7	8.3203	6.6023	1.7638	7.2996	3.4479	2.4032	-0.3596	-1.0989	-0.4172	1.9149	-0.1727	-1.7696	-0.8591	1.1969	0.1079	1.009	0.1667	-0.3831	0.915	-0.0642	0.6398	24.8033	-13.541	57.3709
8	4.9482	2.5338	0.1244	2.7109	-2.7731	6.1379	-0.2402	0.3584	0.5973	0.0614	-0.1009	-0.6772	-0.4325	0.598	0.239	0.3889	-0.0052	-0.0949	0.3682	0.0353	0.773	27.9663	-3.5497	44.8567
9	4.9688	0.3377	0.2434	8.1001	-1.0297	4.1305	0.25	-0.0797	-0.5893	0.2483	-0.0148	0.8838	0.6271	-0.3865	-0.1985	0.334	-0.0724	-0.0211	0.236	0.041	0.3775	-9.1892	-15.0756	41.1487
10	3.2078	2.2867	-2.5973	4.9909	-1.5774	2.8243	0.0128	-0.3674	-0.8491	0.3556	-0.4267	-0.1967	0.3367	0.1471	0.378	0.5456	-0.0238	-0.0361	0.3242	0.0141	0.4564	0.5541	-17.6353	38.0794
11	2.3134	-1.5778	1.4132	2.7389	-4.0664	7.5896	0.0682	0.0219	-0.0347	-0.5673	0.1496	0.1786	0.3841	-0.4329	-0.211	0.2762	-0.071	0.0164	0.2714	-0.0299	0.27	-3.5142	-4.5832	31.3699
12	6.1686	0.8023	-4.2931	9.5086	-0.5957	9.6369	-0.387	0.1973	0.2935	0.1164	-0.0395	0.4351	-0.7725	-0.62	0.4713	0.2251	-0.0208	-0.0788	0.2035	-0.0097	0.2981	1.6769	3.3194	39.7107
13	7.1744	0.9135	2.1906	6.3672	-2.4087	2.3174	-0.4954	-0.914	0.2935	0.8807	0.3736	-1.2797	0.0024	-0.0022	0.0262	0.5162	0.1651	0.0225	0.3948	-0.0937	0.3998	-3.6784	7.7305	53.4751
14	9.4155	-1.6596	0.4398	9.2477	6.6838	8.5516	0.6978	0.4738	0.1898	-1.3687	-0.6827	0.7547	-1.0589	-0.2974	-0.0756	0.4475	0.1128	-0.0533	0.2879	-0.0015	0.4496	-8.8433	10.1156	37.7957
15	2.9604	-3.1307	-2.9282	5.322	6.7701	9.7215	0.1403	-0.5102	0.4786	1.1886	0.2515	0.1174	0.7234	-1.0564	-0.1037	0.5445	0.0217	0.1005	0.4814	-0.0357	0.4481	-10.9563	3.8875	50.7057
16	7.2684	3.5076	-0.1537	5.8582	5.0761	8.0456	0.2079	-0.0915	-0.2978	0.7556	-0.5133	0.9136	0.5185	-0.8709	0.2342	0.427	-0.0006	0.1254	0.3617	-0.0387	0.4344	-17.4143	-0.6169	44.7702
17	8.521	0.9594	-1.8091	5.3536	0.9878	4.0221	0.3336	1.3106	0.7119	-1.0414	-0.6949	0.1963	-1.3919	-0.3748	0.3473	1.2716	0.0449	-0.0841	0.858	0.3333	0.6981	-4.0048	18.8997	6.2199
18	5.3486	1.1757	-0.6767	4.6935	-1.4701	5.2948	0.1293	0.7961	0.4578	-0.3385	-0.2858	-0.0905	-1.1669	0.106	0.1429	0.6891	0.0523	-0.0921	0.5611	0.102	0.3287	-5.4706	10.2159	11.0237
19	0.823	1.55	-0.6362	3.0337	-1.1911	2.3521	0.2783	0.6901	-0.3637	-0.0934	-0.1519	0.6968	0.0134	-0.4198	-0.0178	0.421	0.1569	-0.1436	0.7285	-0.1462	0.5944	-23.54	2.3915	8.2328
20	8.899	3.6955	2.4316	2.8834	0.5503	1.1619	1.0902	-0.7341	-0.1624	1.2568	-0.8296	1.0786	0.0915	-1.3956	-0.062	0.5363	-0.024	0.1015	0.9346	-0.066	0.894	-23.2415	2.4941	20.2794
21	1.7729	-1.4321	1.5988	1.8385	-1.6271	1.5786	-0.3716	0.3971	0.472	0.2647	-0.1806	1.8956	-1.1809	-1.5662	0.5285	0.8187	0.3529	-0.0979	1.1523	-0.309	1.1318	-26.5625	11.7037	14.2992
22	7.3393	-0.9807	2.3228	6.4744	-3.1957	7.9867	-0.3972	0.1747	0.9899	0.2671	-0.1322	0.8093	-2.4131	-1.0724	0.7603	1.1995	0.2398	-0.2028	0.8602	-0.3878	0.7895	-16.4113	20.988	17.5805
23	5.9829	2.4555	-1.3887	5.0625	-1.6741	8.351	-0.0205	0.6195	-0.2704	-1.0921	-0.0322	1.5233	0.6769	-1.6518	-0.0381	0.7888	0.0042	-0.3459	0.7789	-0.2776	1.011	-18.3257	-15.6403	-0.4979
24	8.4259	0.2898	2.5395	7.8403	-4.9317	3.9768	-0.3304	0.1937	-0.2528	-0.0345	0.0934	1.673	0.6177	-1.7034	0.0974	0.9014	0.0469	-0.2073	1.1527	-0.4358	1.0348	-23.5358	-14.9241	3.8769
25	7.7195	0.5179	-2.3634	7.7	-1.1101	6.6611	0.3138	0.4073	-0.7452	-0.0519	-0.7267	0.1978	0.4673	-0.3809	0.3266	0.5512	0.0493	-0.1431	0.4784	-0.1277	0.5134	-11.5702	-11.9153	8.4522
26	7.1387	0.657	1.1257	9.9419	-4.6478	2.4807	0.0902	0.8594	0.5422	-1.3115	-1.1354	-1.1211	0.2085	-0.3191	0.8398	0.6918	0.1978	-0.0701	0.739	-0.0652	0.477	-4.8123	0.3311	2.0228
27	0.2942	-0.3991	0.2321	0.5221	-0.2924	0.1858	0.181	0.5509	0.6799	-1.0608	0.3727	0.7932	-0.3841	-0.2201	-0.3088	1.3048	0.3836	-0.2057	1.3923	-0.1185	0.9061	-14.9018	6.0154	-12.2411
28	7.2537	4.134	-4.4899	7.8562	-4.947	3.8364	0.1416	0.1301	0.2659	-1.3097	-0.9747	-1.371	-0.2741	1.1128	0.8102	1.0223	0.1059	0.1214	0.8076	-0.0832	0.6797	-0.5492	-1.7119	-9.2852
29	3.6039	0.5003	1.2148	3.6112	-3.3401	5.6859	-0.0793	0.1948	0.67	-0.6349	0.2576	1.0387	0.6277	0.3471	0.0936	1.1913	0.1761	-0.1374	0.7043	-0.0905	0.6939	-10.54	-4.3764	-13.8164
30	2.5981	2.368	2.1061	7.2598	-0.132	2.5137	-0.263	0.9647	-0.5471	-1.9247	0.2954	0.5304	0.4519	0.3944	0.008	1.2036	0.3318	0.0431	0.9074	-0.2866	0.6942	-7.3748	-13.2305	-13.3372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 4:27)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 28:59)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 60:113)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 114:154)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 155:166)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 167:179)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 180:193)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 194:219)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 4:37)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 38:73)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 74:97)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 98:113)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 114:154)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 155:166)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 167:193)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 194:217)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 4:15)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 16:98)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 99:154)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 155:166)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 167:204)
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 205:213)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 4:28)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 29:59)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 60:97)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 98:109)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 110:145)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 146:166)
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 167:193)
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 194:213)

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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