PDB-4f0b: Crystal structure of the glutathione transferase URE2P1 from Phan...

ID or keywords:

Entry

Database: PDB / ID: 4f0b

Title

Crystal structure of the glutathione transferase URE2P1 from Phanerochaete chrysosporium.

Components

THIOL TRANSFERASE

Keywords

TRANSFERASE / THIOL TRANSFERASE / GST fold / oxydized glutathione

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Didierjean, C. / Favier, F. / Roret, T.

Citation

Journal: Febs Lett. / Year: 2013
Title: Atypical features of a Ure2p glutathione transferase from Phanerochaete chrysosporium.
Authors: Thuillier, A. / Roret, T. / Favier, F. / Gelhaye, E. / Jacquot, J.P. / Didierjean, C. / Morel-Rouhier, M.

History

Deposition	May 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f0b.cif.gz	201.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4f0b.ent.gz	162.3 KB	Display	PDB format
PDBx/mmJSON format	4f0b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f0b_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4f0b_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4f0b_validation.xml.gz	23.1 KB	Display
Data in CIF	4f0b_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/4f0b ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f0b	HTTPS FTP

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Related structure data

Related structure data	3gxoS 4f0c S: Starting model for refinement
Similar structure data	6x85-2 7kp9-d 7d6a-1 6xm8-d 3gx0-1 6op0-d 4iel-2 3vwx-1 2zjc-d 1jtz-d 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 (8) #255 - Mar 2021 Cisplatin and DNA similarity (7)

Deposited unit

A: THIOL TRANSFERASE

B: THIOL TRANSFERASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.907, 53.947, 165.225
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	THIOL TRANSFERASE Mass: 25440.002 Da / Num. of mol.: 2 / Fragment: PcUre2p1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: I7A570*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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.23 Å³/Da / Density % sol: 44.83 %
Crystal grow	Temperature: 277 K / Method: microbatch / pH: 5.6 Details: 20% (v/v) 2-propanol, 20% (w/v) PEG-4000, 0.1M sodium citrate tribasic dihydrate, pH 5.6, MICROBATCH, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980557 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2011 / Details: mirrors
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980557 Å / Relative weight: 1
Reflection	Resolution: 1.45→48.65 Å / Num. all: 77259 / Num. obs: 77259 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / R_merge(I) obs: 0.026 / Net I/σ(I): 24.9
Reflection shell	Resolution: 1.45→1.53 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.262 / Mean I/σ(I) obs: 7.3 / % possible all: 81.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GXO

3gxo

Resolution: 1.45→45.169 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 13.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1649	3868	5.01 %	RANDOM
R_work	0.1408	-	-	-
all	0.142	77182	-	-
obs	0.142	77182	94.53 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 59.934 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2988 Å²	0 Å²	-0 Å²
2-	-	2.6376 Å²	0 Å²
3-	-	-	-2.3388 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→45.169 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3542	0	92	516	4150

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3883
X-RAY DIFFRACTION	f_angle_d	1.456	5286
X-RAY DIFFRACTION	f_dihedral_angle_d	15.95	1458
X-RAY DIFFRACTION	f_chiral_restr	0.098	540
X-RAY DIFFRACTION	f_plane_restr	0.009	703

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 (%)
1.45-1.4675	0.2655	94	0.1852	1736	X-RAY DIFFRACTION	65
1.4675-1.4861	0.2019	111	0.1724	2088	X-RAY DIFFRACTION	75
1.4861-1.5056	0.1809	116	0.1673	2285	X-RAY DIFFRACTION	84
1.5056-1.5262	0.1701	150	0.151	2579	X-RAY DIFFRACTION	95
1.5262-1.5481	0.1638	136	0.1394	2630	X-RAY DIFFRACTION	95
1.5481-1.5712	0.1653	126	0.136	2619	X-RAY DIFFRACTION	96
1.5712-1.5957	0.1504	120	0.1257	2613	X-RAY DIFFRACTION	94
1.5957-1.6219	0.1452	126	0.1248	2661	X-RAY DIFFRACTION	97
1.6219-1.6498	0.1451	132	0.1216	2620	X-RAY DIFFRACTION	95
1.6498-1.6798	0.1408	137	0.1207	2635	X-RAY DIFFRACTION	97
1.6798-1.7122	0.1485	145	0.1171	2600	X-RAY DIFFRACTION	96
1.7122-1.7471	0.1494	144	0.1204	2659	X-RAY DIFFRACTION	96
1.7471-1.7851	0.1345	146	0.1166	2623	X-RAY DIFFRACTION	96
1.7851-1.8266	0.1311	133	0.1159	2664	X-RAY DIFFRACTION	97
1.8266-1.8723	0.1434	138	0.1272	2654	X-RAY DIFFRACTION	96
1.8723-1.9229	0.1656	139	0.1331	2694	X-RAY DIFFRACTION	97
1.9229-1.9795	0.1826	169	0.1323	2631	X-RAY DIFFRACTION	97
1.9795-2.0434	0.1649	137	0.1343	2683	X-RAY DIFFRACTION	97
2.0434-2.1164	0.1615	129	0.1348	2708	X-RAY DIFFRACTION	97
2.1164-2.2012	0.159	143	0.1323	2694	X-RAY DIFFRACTION	98
2.2012-2.3014	0.1519	165	0.1329	2696	X-RAY DIFFRACTION	98
2.3014-2.4227	0.1451	139	0.1387	2717	X-RAY DIFFRACTION	97
2.4227-2.5745	0.1758	152	0.1402	2737	X-RAY DIFFRACTION	98
2.5745-2.7732	0.1628	147	0.1448	2740	X-RAY DIFFRACTION	99
2.7732-3.0522	0.1612	149	0.1454	2753	X-RAY DIFFRACTION	98
3.0522-3.4937	0.1542	148	0.1369	2781	X-RAY DIFFRACTION	98
3.4937-4.4012	0.1619	150	0.1401	2833	X-RAY DIFFRACTION	99
4.4012-45.1912	0.2296	147	0.1918	2981	X-RAY DIFFRACTION	98

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	0.7179	0.0373	0.0443	0.5742	-0.1096	0.5193	-0.0832	-0.3456	-0.1662	0.1947	0.0195	-0.0681	0.1202	0.1143	-0.0351	0.0943	0.0275	-0.0106	0.1469	0.0365	0.0657	41.1646	26.1472	36.6476
2	1.9651	0.7313	0.5186	0.949	0.2796	1.0145	-0.0954	-0.1846	-0.2395	0.0116	0.0304	-0.061	0.1751	0.0482	-0.0325	0.1358	0.0007	0.0164	0.1266	0.0501	0.0806	32.3554	20.7882	36.1057
3	1.4328	0.4857	-0.2666	1.2321	-0.5636	1.1203	-0.0441	-0.2302	-0.0905	0.0999	0.0593	0.1124	0.0792	-0.3151	0.0086	0.0822	-0.0187	0.0108	0.1466	0.0367	0.061	22.543	24.0651	34.8601
4	0.847	0.0699	-0.0496	0.6128	0.0076	1.0116	0.0393	-0.4463	0.0708	0.1374	-0.0249	-0.0289	-0.0024	0.0729	-0.0085	0.076	0.0007	-0.0049	0.1447	-0.0042	0.0333	36.596	35.5277	36.9717
5	0.9428	-0.6995	0.159	3.4473	-0.9482	0.5881	0.0234	-0.3678	0.1342	0.2424	-0.0074	-0.0793	-0.2051	0.1912	0.0101	0.1135	-0.0178	-0.0269	0.1798	-0.0446	0.1111	49.4103	42.405	32.7402
6	1.3029	0.1847	0.3938	1.4857	0.615	1.5523	-0.0452	0.0009	0.0945	0.0244	0.0576	-0.1495	-0.1089	0.1273	-0.0119	0.0413	0.0012	-0.0039	0.0432	-0.0069	0.0513	41.8471	41.3365	22.1894
7	0.9062	0.0722	0.0415	1.2554	0.1431	1.1917	0.0319	0.0029	-0.2047	-0.0928	0.0251	0.0321	0.2015	-0.1094	0.0097	0.0824	-0.0111	-0.0209	0.038	0.004	0.0867	28.8746	21.1201	13.4199
8	1.9073	0.5851	0.3232	0.6176	0.0728	0.5646	0.0011	0.0357	-0.1592	-0.0806	0.0009	-0.0467	0.0539	0.0304	-0.0154	0.0661	0.0101	0.0057	0.0303	-0.0071	0.0524	37.6136	28.3407	8.034
9	1.2915	-0.0391	-0.1228	0.5454	-0.039	1.0476	-0.002	-0.039	-0.0724	-0.0402	0.0226	-0.0341	0.1012	0.1335	-0.0061	0.0439	0.0108	0.0014	0.0528	0.0013	0.0543	46.2788	28.8018	20.4047
10	0.8424	-0.0613	-0.1083	0.594	-0.2782	1.4834	-0.0076	-0.0514	-0.1906	-0.0167	-0.0104	-0.0357	0.2319	0.1816	0.0178	0.081	0.0307	0.0084	0.0648	0.0069	0.1068	48.1865	22.1164	20.5626
11	0.681	-0.171	0.126	0.7696	0.3682	1.0801	0.0208	0.0628	0.2978	-0.0367	0.0093	-0.0593	-0.2421	-0.0125	0.0104	0.0767	-0.0021	0.0109	0.0188	-0.0111	0.1076	31.518	56.225	15.3985
12	0.695	-0.0565	-0.1204	2.8502	2.2575	2.8591	0.0161	0.0906	0.1185	-0.0773	0.0139	-0.0825	-0.1874	-0.1193	0.0225	0.0917	0.0042	0.0048	0.055	0.0068	0.0644	32.704	52.3485	6.075
13	0.8127	-0.0134	-0.089	0.5241	0.072	1.0097	0.0081	0.0032	0.0911	-0.0245	0.0037	-0.0576	-0.087	0.0919	-0.0068	0.0423	-0.0094	0.0073	0.0259	0.0017	0.0607	39.4509	48.4489	12.436
14	1.3061	-0.7636	0.6419	1.4369	-1.0071	1.767	-0.0273	-0.1445	0.2718	0.073	-0.036	-0.2201	-0.2845	0.1787	0.0274	0.1214	-0.0233	-0.0028	0.1452	-0.0645	0.1237	33.9867	53.9384	34.0432
15	1.0197	0.222	0.5885	0.7716	0.5262	1.6971	0.019	-0.0401	0.0149	-0.0042	-0.0197	0.0463	0.0438	-0.0517	0.0028	0.0235	0.0015	0.008	0.0179	0.007	0.0412	25.7609	36.375	19.0602
16	0.7752	-0.0331	-0.03	1.5079	0.9788	1.8553	0.037	-0.0755	-0.0464	0.0274	-0.0579	0.0619	0.0348	-0.1453	0.0218	0.0337	-0.0152	-0.0033	0.0648	0.0143	0.0581	17.2122	31.6555	20.6909
17	1.6733	0.3309	-0.6722	1.0766	-0.4635	1.7175	0.0975	-0.0773	0.1272	0.1177	-0.0546	0.1738	0.025	-0.2647	-0.0162	0.0722	-0.0068	0.0172	0.1155	-0.0512	0.072	19.7919	48.7585	32.0301
18	1.9194	0.3182	-0.4126	1.7432	-0.0137	0.3971	-0.0296	0.0294	0.0954	-0.0787	-0.0294	0.0763	-0.0309	-0.1828	-0.0005	0.0393	0.0025	0.0094	0.0432	-0.0044	0.0419	20.6101	44.5912	17.8407
19	0.8663	0.4129	-0.184	1.0866	-0.2756	0.4538	0.0165	-0.0164	0.1559	-0.0435	-0.0236	0.149	-0.0766	-0.0833	-0.0186	0.0624	0.0156	-0.0015	0.0793	-0.0104	0.0841	15.6624	49.6131	19.4797

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:33)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 34:49)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 50:72)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 73:95)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 96:108)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 109:124)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 125:144)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 145:166)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 167:193)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 194:224)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 5:33)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 34:49)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 50:95)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 96:108)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 109:144)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 145:166)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 167:177)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 178:193)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 194:224)

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