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

ID or keywords:

Entry

Database: PDB / ID: 4zbb

Title

Crystal structure of the glutathione transferase URE2P8 from Phanerochaete chrysosporium complexed with glutathionyl-S-dinitrobenzene.

Components

PcUre2p8

Keywords

TRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD / GLUTATHIONE S-(2 / 4 DINITROBENZENE)

Function / homology

Function and homology information

glutathione transferase
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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	4zbb.cif.gz	425.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4zbb.ent.gz	349.8 KB	Display	PDB format
PDBx/mmJSON format	4zbb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zbb_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	4zbb_full_validation.pdf.gz	2.7 MB	Display
Data in XML	4zbb_validation.xml.gz	48.1 KB	Display
Data in CIF	4zbb_validation.cif.gz	68.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbb ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbb	HTTPS FTP

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Related structure data

Related structure data	4f0cC 4zb6C 4zb7C 4zb8C 4zb9C 4zbaSC 4zbdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zba-2 4zba-1 7db0-d 2hay-2 6kem-d 6keq-d 3zmk-2 3lxz-2 6oc6-1 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 - 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

C: PcUre2p8

B: PcUre2p8

D: PcUre2p8

hetero molecules

109 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
54.6 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
54.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.451, 92.156, 184.734
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ACBD

#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

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Non-polymers , 5 types, 1056 molecules

#2: Chemical	ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE) Mass: 473.415 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₆H₁₉N₅O₁₀S
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1033 / 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: 2.17 Å³/Da / Density % sol: 43.33 %
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: Nov 14, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 1.8→46.3 Å / Num. obs: 85430 / % possible obs: 99.4 % / Redundancy: 18.9 % / R_merge(I) obs: 0.065 / Net I/σ(I): 6.5
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.325 / Mean I/σ(I) obs: 5.1 / Num. unique all: 11918 / % possible all: 96.5

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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: 1.8→46.263 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1809	4270	5 %
R_work	0.1662	-	-
obs	0.1669	85327	99.34 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.775 Å² / k_sol: 0.391 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.0941 Å²	-0 Å²	0 Å²
2-	-	-2.0407 Å²	-0 Å²
3-	-	-	6.0394 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.263 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7344	0	308	1033	8685

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	7929
X-RAY DIFFRACTION	f_angle_d	0.771	10732
X-RAY DIFFRACTION	f_dihedral_angle_d	17.434	2921
X-RAY DIFFRACTION	f_chiral_restr	0.043	1080
X-RAY DIFFRACTION	f_plane_restr	0.015	1388

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 (%)
1.7973-1.8177	0.2734	148	0.24	2297	X-RAY DIFFRACTION	88
1.8177-1.8391	0.2604	132	0.2266	2720	X-RAY DIFFRACTION	98
1.8391-1.8615	0.264	139	0.2143	2598	X-RAY DIFFRACTION	99
1.8615-1.8851	0.2223	140	0.2042	2657	X-RAY DIFFRACTION	99
1.8851-1.9099	0.2099	142	0.1946	2699	X-RAY DIFFRACTION	99
1.9099-1.9361	0.1908	143	0.1847	2632	X-RAY DIFFRACTION	99
1.9361-1.9637	0.2158	154	0.1812	2665	X-RAY DIFFRACTION	100
1.9637-1.993	0.1983	145	0.1845	2677	X-RAY DIFFRACTION	100
1.993-2.0242	0.1936	145	0.1768	2658	X-RAY DIFFRACTION	100
2.0242-2.0574	0.2116	135	0.1751	2741	X-RAY DIFFRACTION	100
2.0574-2.0928	0.2084	131	0.1737	2678	X-RAY DIFFRACTION	100
2.0928-2.1309	0.2349	123	0.1776	2719	X-RAY DIFFRACTION	100
2.1309-2.1719	0.1795	141	0.167	2690	X-RAY DIFFRACTION	100
2.1719-2.2162	0.1967	129	0.1634	2693	X-RAY DIFFRACTION	100
2.2162-2.2644	0.2002	142	0.1656	2696	X-RAY DIFFRACTION	100
2.2644-2.3171	0.1644	141	0.1691	2733	X-RAY DIFFRACTION	100
2.3171-2.375	0.1955	131	0.1677	2704	X-RAY DIFFRACTION	100
2.375-2.4392	0.1648	153	0.1667	2682	X-RAY DIFFRACTION	100
2.4392-2.511	0.1795	136	0.1631	2698	X-RAY DIFFRACTION	100
2.511-2.592	0.2045	156	0.1655	2699	X-RAY DIFFRACTION	100
2.592-2.6847	0.1762	124	0.1674	2772	X-RAY DIFFRACTION	100
2.6847-2.7922	0.1844	170	0.1619	2681	X-RAY DIFFRACTION	100
2.7922-2.9192	0.1894	154	0.1598	2695	X-RAY DIFFRACTION	100
2.9192-3.0731	0.1628	122	0.164	2768	X-RAY DIFFRACTION	100
3.0731-3.2656	0.1478	132	0.1581	2746	X-RAY DIFFRACTION	100
3.2656-3.5176	0.1635	151	0.1451	2744	X-RAY DIFFRACTION	100
3.5176-3.8715	0.1377	144	0.1395	2783	X-RAY DIFFRACTION	100
3.8715-4.4313	0.1278	158	0.1307	2785	X-RAY DIFFRACTION	100
4.4313-5.5814	0.1688	147	0.1494	2794	X-RAY DIFFRACTION	100
5.5814-46.2786	0.2083	162	0.2054	2953	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	0.9268	-0.3342	-0.1018	0.4902	0.1817	0.5428	-0.0351	-0.1067	-0.1175	0.109	0.0202	0.0301	0.1026	-0.0347	0.0295	0.1066	0.0072	0.0018	0.0896	0.009	0.0722	21.8289	100.4709	33.3364
2	0.7966	-0.1386	-0.0984	0.6068	0.0023	0.4361	-0.0155	-0.089	0.114	0.0944	0.0048	-0.0535	-0.014	0.048	0.0235	0.0779	0.003	-0.0166	0.0836	-0.0144	0.0611	28.0885	118.6103	30.9759
3	0.5877	-0.1679	0.0151	1.332	-0.281	0.6066	0.0405	-0.2576	0.0396	0.3006	0.006	-0.1958	-0.0195	0.1779	0.0451	0.1736	0.0041	-0.0525	0.2138	-0.0375	0.1252	31.6621	116.7977	44.1755
4	0.9333	0.0633	0.5139	0.9218	0.3639	0.8935	0.0228	0.1217	0.1458	-0.1809	-0.0298	0.0091	-0.2233	-0.06	0.0148	0.1621	0.033	0.0306	0.134	0.0337	0.1011	48.8613	82.5057	11.6434
5	0.5251	-0.0169	0.0497	0.4615	0.0083	0.3878	0.0479	0.0421	0.0508	0.0209	-0.0173	0.003	-0.0843	-0.0271	0.0046	0.102	0.0099	0.0188	0.0869	0.0118	0.1033	45.8051	75.4885	26.3108
6	0.3637	-0.1215	-0.2404	1.1367	-0.708	1.7714	0.0293	0.0326	0.1718	0.072	0.0101	0.0418	-0.2576	-0.2049	-0.0208	0.1798	0.0479	0.0348	0.1172	-0.0053	0.1556	39.1457	87.9466	28.4114
7	2.0837	-0.1151	0.1271	0.803	0.2052	1.1636	-0.0134	0.1238	0.1462	-0.1679	0.037	0.052	-0.0706	0.0054	0.0238	0.1008	0.0131	-0.007	0.0644	0.008	0.0836	21.7419	126.5204	7.978
8	0.563	-0.0037	-0.0024	0.6932	-0.0419	0.2893	0.0053	0.0283	0.008	-0.0739	-0.0191	-0.0096	-0.0035	0.0119	0.0238	0.0832	0.0034	-0.0005	0.0727	0.0001	0.05	26.2429	114.744	12.8398
9	5.016	0.3657	0.2618	1.7382	0.0866	2.2497	-0.0385	0.1904	0.0791	-0.3551	0.0694	-0.0776	-0.1392	0.2168	0.0237	0.2188	0.0147	0.0403	0.1328	0.0131	0.0888	28.8139	122.7237	-1.31
10	1.2591	-0.2157	-0.4504	0.6543	0.2516	0.6975	-0.0268	-0.0685	-0.2414	0.112	-0.0249	0.0152	0.0614	-0.0265	-0.004	0.1247	-0.0076	-0.0048	0.095	0.0241	0.1209	48.8356	52.4965	33.9911
11	0.8161	-0.1779	-0.006	0.5843	-0.039	0.255	-0.0024	-0.1223	-0.0398	0.0755	-0.0181	-0.0238	0.0105	0.0467	-0.0062	0.1018	-0.0059	-0.0071	0.1218	0.0171	0.0897	53.764	61.2243	34.5129
12	0.8261	-0.0502	0.0088	0.5066	-0.0501	0.354	0.019	0.0764	-0.0801	-0.0597	-0.0187	0.0081	0.0052	-0.0083	-0.0078	0.0796	0.0172	-0.0024	0.0982	-0.007	0.0871	47.005	60.6962	15.6625
13	1.277	0.0871	0.0995	0.479	-0.0593	0.7593	0.0695	0.2308	-0.3204	-0.1308	-0.0823	0.1938	0.109	-0.1174	-0.0771	0.1232	0.0187	-0.0263	0.1826	-0.0644	0.1737	46.8208	50.9157	7.7688
14	3.4084	-0.1062	-1.2225	0.7055	0.1681	1.3142	-0.1391	-0.0344	-0.4207	0.163	-0.0845	0.1723	0.2569	-0.1827	0.0659	0.1478	-0.0187	0.029	0.1452	-0.0054	0.3381	47.7452	43.1571	24.8388

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:74)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 75:183)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 184:222)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 3:60)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 61:183)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 184:223)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 3:28)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 29:206)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 207:223)
10	X-RAY DIFFRACTION	10	chain 'D' and (resseq 3:51)
11	X-RAY DIFFRACTION	11	chain 'D' and (resseq 52:86)
12	X-RAY DIFFRACTION	12	chain 'D' and (resseq 87:183)
13	X-RAY DIFFRACTION	13	chain 'D' and (resseq 184:206)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 207:222)

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