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

ID or keywords:

Entry

Database: PDB / ID: 4zba

Title

Crystal structure of the glutathione transferase URE2P8 from Phanerochaete chrysosporium with oxidized glutathione.

Components

PcUre2p8

Keywords

TRANSFERASE /

GLUTATHIONE TRANSFERASE / GST FOLD / OXYDIZED GLUTATHIONE

Function / homology

Function and homology information

Glutathione S-transferase, C-terminal domain /

Glutathione S-transferase, N-terminal domain /

Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 /

Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. /

Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. /

Glutathione S-transferase, N-terminal ...
Similarity search - Domain/homology

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.501 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	4zba.cif.gz	415.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4zba.ent.gz	342.1 KB	Display	PDB format
PDBx/mmJSON format	4zba.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/zb/4zba ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zba	HTTPS FTP

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Related structure data

Related structure data	4f0cSC 4zb6C 4zb7C 4zb8C 4zb9C 4zbbC 4zbdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6oc6-1 4zbb-1 4zbb-2 5m8t-3 3zmk-2 4f0c-1 1v2a-1 6z1m-2 3gno-d 3lg6-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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 (10) #255 - Mar 2021 Cisplatin and DNA similarity (8)

Deposited unit

A: PcUre2p8

B: PcUre2p8

C: PcUre2p8

D: PcUre2p8

hetero molecules

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

1

A: PcUre2p8

B: PcUre2p8

hetero molecules

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

2

C: PcUre2p8

D: PcUre2p8

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.641, 91.872, 180.014
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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 / Glutathione disulfide Mass: 612.631 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₃₂N₆O₁₂S₂
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1538 / 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: 2.12 Å³/Da / Density % sol: 41.87 %
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: May 10, 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: 1.5→46.3 Å / Num. obs: 136502 / % possible obs: 95.9 % / Redundancy: 7 % / R_merge(I) obs: 0.044 / Net I/σ(I): 25.8
Reflection shell	Resolution: 1.5→1.6 Å / R_merge(I) obs: 0.232 / Mean I/σ(I) obs: 4.9 / Num. unique all: 15653 / % possible all: 77.1

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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: 4F0C

4f0c

Resolution: 1.501→46.3 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1689	6827	5.01 %
R_work	0.1497	-	-
obs	0.1507	136395	95.59 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.4 Å² / k_sol: 0.398 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.874 Å²	-0 Å²	-0 Å²
2-	-	1.1434 Å²	0 Å²
3-	-	-	0.7307 Å²

Refinement step

Cycle: LAST / Resolution: 1.501→46.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7366	0	177	1538	9081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8134
X-RAY DIFFRACTION	f_angle_d	1.109	11045
X-RAY DIFFRACTION	f_dihedral_angle_d	15.374	3014
X-RAY DIFFRACTION	f_chiral_restr	0.077	1120
X-RAY DIFFRACTION	f_plane_restr	0.006	1441

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 (%)
1.5011-1.5182	0.2364	163	0.2144	2973	X-RAY DIFFRACTION	67
1.5182-1.536	0.2361	158	0.2019	3311	X-RAY DIFFRACTION	73
1.536-1.5548	0.1933	180	0.1807	3483	X-RAY DIFFRACTION	78
1.5548-1.5745	0.2017	187	0.176	3639	X-RAY DIFFRACTION	82
1.5745-1.5952	0.1913	208	0.17	3843	X-RAY DIFFRACTION	86
1.5952-1.617	0.1934	226	0.1721	3985	X-RAY DIFFRACTION	89
1.617-1.6401	0.2168	207	0.1715	4182	X-RAY DIFFRACTION	93
1.6401-1.6646	0.2148	235	0.1662	4406	X-RAY DIFFRACTION	99
1.6646-1.6906	0.1776	252	0.1622	4421	X-RAY DIFFRACTION	100
1.6906-1.7184	0.1801	233	0.1592	4508	X-RAY DIFFRACTION	100
1.7184-1.748	0.1707	217	0.1542	4482	X-RAY DIFFRACTION	100
1.748-1.7798	0.1759	198	0.1543	4512	X-RAY DIFFRACTION	100
1.7798-1.814	0.1796	260	0.151	4447	X-RAY DIFFRACTION	100
1.814-1.851	0.1799	228	0.146	4544	X-RAY DIFFRACTION	100
1.851-1.8913	0.1866	274	0.1458	4423	X-RAY DIFFRACTION	100
1.8913-1.9353	0.1613	252	0.1515	4512	X-RAY DIFFRACTION	100
1.9353-1.9837	0.1608	237	0.1549	4462	X-RAY DIFFRACTION	100
1.9837-2.0373	0.1898	245	0.1582	4489	X-RAY DIFFRACTION	100
2.0373-2.0973	0.1834	229	0.1593	4499	X-RAY DIFFRACTION	100
2.0973-2.165	0.1673	235	0.1494	4529	X-RAY DIFFRACTION	100
2.165-2.2423	0.1648	210	0.1496	4562	X-RAY DIFFRACTION	100
2.2423-2.3321	0.1725	253	0.1467	4498	X-RAY DIFFRACTION	100
2.3321-2.4382	0.1513	259	0.1374	4544	X-RAY DIFFRACTION	100
2.4382-2.5668	0.1516	236	0.1448	4502	X-RAY DIFFRACTION	100
2.5668-2.7276	0.1674	258	0.1544	4541	X-RAY DIFFRACTION	100
2.7276-2.9381	0.1939	230	0.1448	4566	X-RAY DIFFRACTION	100
2.9381-3.2337	0.1662	231	0.1468	4578	X-RAY DIFFRACTION	100
3.2337-3.7015	0.1401	215	0.1297	4634	X-RAY DIFFRACTION	100
3.7015-4.6628	0.133	246	0.1222	4660	X-RAY DIFFRACTION	100
4.6628-46.3453	0.1715	265	0.1659	4833	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	2.5316	-0.3132	-0.458	0.5562	0.1086	1.5363	-0.0527	-0.0815	-0.127	0.1326	0.0288	0.0317	0.1673	-0.0536	0.0028	0.0878	-0.0196	0.0039	0.0762	0.0013	0.045	20.7604	102.0565	37.6835
2	1.3689	-0.3672	-0.3077	0.6675	-0.1406	0.8503	0.0039	-0.0742	-0.1416	0.0272	-0.0657	0.0401	0.1666	0.019	0.0809	0.0867	-0.0207	-0.0001	0.0583	-0.0024	0.0769	25.8573	96.7337	30.4783
3	0.308	0.0825	-0.0138	1.0087	0.0625	0.482	0.0306	-0.0326	-0.0198	0.0447	-0.0632	0.118	-0.0112	-0.1094	0.0297	0.054	-0.0148	0.0022	0.1025	-0.018	0.0644	15.0037	112.1025	29.4768
4	1.0265	-0.011	-0.2567	0.7644	0.2151	0.854	0.0269	-0.0931	0.0351	0.0595	-0.0037	-0.0849	-0.0102	0.1546	-0.021	0.0612	-0.0198	-0.0113	0.0998	-0.0187	0.0573	35.0286	118.2025	31.6508
5	0.0879	-0.0019	-0.1847	0.3717	-0.0877	0.4363	0.0425	-0.0495	0.0015	0.0817	0.0672	-0.2219	-0.149	0.4243	-0.1287	0.0886	-0.0836	-0.0131	0.268	-0.1146	0.1136	33.7104	123.1361	42.4943
6	3.3045	-0.647	0.2263	0.7863	-0.2225	0.0655	0.0637	-0.2757	-0.2113	0.2926	0.0882	-0.1278	0.1838	0.2634	-0.1012	0.1508	0.0219	-0.054	0.2114	-0.0088	0.1155	30.8075	104.0883	46.4605
7	1.5175	0.2537	0.4016	0.7372	0.1363	0.8848	-0.0273	0.0439	0.1771	-0.1233	-0.0181	-0.0107	-0.1386	0.0316	0.0538	0.098	0.0079	0.0027	0.0559	-0.0027	0.0705	25.4904	128.6002	11.775
8	0.3949	-0.1723	0.0944	1.2304	-0.0698	0.4054	0.026	-0.0352	0.0314	-0.0891	-0.0364	0.1206	-0.0181	-0.0719	0.0087	0.0609	0.008	-0.0061	0.0811	-0.0162	0.064	14.8806	117.6386	17.1179
9	2.3376	-0.6573	0.5026	1.201	-0.1694	1.9769	0.0448	-0.0892	0.1148	-0.0002	-0.0379	-0.2603	-0.1853	0.264	-0.0106	0.0796	-0.0095	0.0112	0.1072	-0.0184	0.0939	43.4123	114.6133	15.3277
10	3.6391	1.0185	1.2307	0.9252	0.5944	0.9626	0.0474	0.0277	-0.0557	-0.0511	-0.0101	-0.114	0.0754	0.1249	-0.0233	0.0794	0.0065	0.0132	0.0737	-0.0027	0.0628	35.5785	102.5681	14.3011
11	1.2265	0.0601	0.142	0.7594	0.083	0.5256	-0.0067	0.13	0.0115	-0.1034	0.0094	0.0096	0.0173	-0.038	0.014	0.0779	0.0042	0.0007	0.0662	-0.0132	0.0324	23.4167	107.7333	8.5454
12	1.19	-0.1309	0.0353	1.102	0.0608	0.6599	0.0625	0.1256	-0.1122	-0.1585	-0.0573	-0.0369	0.0528	0.0664	-0.0089	0.1142	0.0126	0.0066	0.0977	-0.0247	0.063	29.815	102.8733	2.3154
13	3.921	1.757	-0.4895	2.5273	-0.5825	1.5827	-0.0091	0.2097	0.1132	-0.2933	0.0246	-0.0095	-0.1911	0.04	-0.0218	0.1866	0.0294	0.0364	0.0862	0.0015	0.0694	28.9206	122.569	-0.9093
14	0.8926	0.0013	0.0459	0.8516	0.171	0.6755	0.0118	0.2296	0.1381	-0.1224	-0.013	-0.0496	-0.1601	0.007	0.0012	0.091	-0.0022	0.0166	0.1378	0.0385	0.0982	53.6836	80.6224	11.966
15	1.0639	0.0304	0.119	0.776	0.1334	0.7098	0.0052	0.0053	0.046	0.018	-0.015	0.0338	-0.059	-0.0631	0.0165	0.0509	0.0088	0.0091	0.0633	0.0065	0.0496	43.8683	74.4536	27.734
16	0.6639	0.0216	-0.1297	1.0151	-0.263	1.5026	0.0005	0.1836	0.1733	-0.1258	-0.0112	0.0636	-0.2223	-0.175	-0.0071	0.1689	0.04	0.0006	0.1385	0.0121	0.1514	40.9557	87.9137	26.3098
17	2.2269	-0.4152	-0.5022	0.7068	0.2331	0.701	-0.0687	-0.1211	-0.3366	0.0702	0.0292	0.0382	0.1163	-0.0098	0.0178	0.0978	0.0004	-0.0045	0.0918	0.019	0.1313	49.9991	51.0521	31.5904
18	0.7858	-0.0015	0.0917	0.4689	-0.0602	0.526	-0.0007	0.057	-0.079	-0.0223	-0.0045	-0.0189	0.0197	-0.0056	0.005	0.0474	0.0028	-0.0008	0.0794	-0.0096	0.0699	49.3494	60.2595	19.8896
19	0.8227	-0.1366	0.4093	1.048	-0.2321	0.8364	0.0554	-0.0229	-0.1994	-0.0828	-0.0516	0.1177	0.1848	-0.2209	-0.0419	0.1249	-0.0176	-0.0206	0.1764	-0.0429	0.1749	47.3533	46.4278	13.8956

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:28)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 29:60)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 61:113)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 114:183)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 184:206)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 207:223)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 3:60)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 61:113)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 114:133)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 134:155)
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 207:223)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 2:86)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 87:183)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 184:223)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 3:47)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 48:183)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 184:223)

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