PDB-4txn: Crystal structure of uridine phosphorylase from Schistosoma manso...

ID or keywords:

Entry

Database: PDB / ID: 4txn

Title

Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with 5-fluorouracil

Components

Uridine phosphorylase

Keywords

TRANSFERASE / Uridine phosphorylase

Function / homology

Function and homology information

uridine catabolic process / nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / identical protein binding / cytosol
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Marinho, A. / Torini, J. / Romanello, L. / Cassago, A. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.M.

Funding support

Brazil, 1items

Citation

Journal: Biochimie / Year: 2016
Title: Analysis of two Schistosoma mansoni uridine phosphorylases isoforms suggests the emergence of a protein with a non-canonical function.
Authors: da Silva Neto, A.M. / Torini de Souza, J.R. / Romanello, L. / Cassago, A. / Serrao, V.H. / DeMarco, R. / Brandao-Neto, J. / Garratt, R.C. / Pereira, H.D.

History

Deposition	Jul 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	May 25, 2016	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 2023	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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PDBx/mmCIF format	4txn.cif.gz	464.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4txn_validation.pdf.gz	470 KB	Display	wwPDB validaton report
Full document	4txn_full_validation.pdf.gz	479.2 KB	Display
Data in XML	4txn_validation.xml.gz	56 KB	Display
Data in CIF	4txn_validation.cif.gz	81.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/4txn ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txn	HTTPS FTP

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Related structure data

Related structure data	4txhC 4txjSC 4txlC 4txmC 5cyfC 5cygC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4txl-1 4txl-2 3whr-d 4txh-2 4txm-d 2xr7-d 4ott-d 3a75-2 6dab-d 2e1u-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

Deposited unit

A: Uridine phosphorylase

B: Uridine phosphorylase

C: Uridine phosphorylase

D: Uridine phosphorylase

hetero molecules

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

1

A: Uridine phosphorylase

B: Uridine phosphorylase

hetero molecules

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

2

C: Uridine phosphorylase

D: Uridine phosphorylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.643, 107.488, 115.576
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

#1: Protein	Uridine phosphorylase Mass: 32649.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_082430 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4VGI0, uridine phosphorylase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-URF / 5-FLUOROURACIL Mass: 130.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₃FN₂O₂ / Comment: medication*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1291 / 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: 2.27 Å³/Da / Density % sol: 45.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 200mM ammonium sulphate, 100mM Bis-tris pH 5.5, 20-25% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 31, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→30 Å / Num. obs: 80105 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge F obs: 0.177 / R_merge(I) obs: 0.098 / R_rim(I) all: 0.114 / Χ²: 0.928 / Net I/σ(I): 11.61 / Num. measured all: 306780

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2-2.12		0.684	0.539	2.41	44454	12909	12190	0.63	94.4
2.12-2.26		0.451	0.364	3.71	45924	12171	12079	0.424	99.2
2.26-2.44		0.326	0.269	5.07	43604	11368	11294	0.312	99.3
2.44-2.68		0.234	0.193	6.99	40827	10508	10450	0.224	99.4
2.68-2.99		0.153	0.129	10.23	37214	9528	9496	0.15	99.7
2.99-3.44		0.082	0.076	16.82	32981	8455	8425	0.088	99.6
3.44-4.2		0.047	0.047	26.27	27791	7206	7165	0.054	99.4
4.2-5.88		0.034	0.036	31.1	21618	5677	5637	0.042	99.3
	5.88	0.023	0.027	36.66	12367	3431	3369	0.031	98.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
PHENIX	(phenix.refine: 1.9_1692)	refinement
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4TXJ

4txj

Resolution: 2→29.016 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2065	4005	5 %	Random selection
R_work	0.1715	76074	-	-
obs	0.1732	80079	98.6 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 66.25 Å² / B_iso mean: 22.385 Å² / B_iso min: 7 Å²

Refinement step

Cycle: final / Resolution: 2→29.016 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8648	0	56	1291	9995
B_iso mean	-	-	15.3	33.16	-
Num. residues	-	-	-	-	1153

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8889
X-RAY DIFFRACTION	f_angle_d	0.865	12048
X-RAY DIFFRACTION	f_chiral_restr	0.032	1408
X-RAY DIFFRACTION	f_plane_restr	0.003	1547
X-RAY DIFFRACTION	f_dihedral_angle_d	11.603	3084

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 (%)
2-2.0215	0.2708	107	0.2351	2017	X-RAY DIFFRACTION	78
2.0215-2.0461	0.2441	135	0.2103	2568	X-RAY DIFFRACTION	99
2.0461-2.072	0.2493	138	0.2074	2625	X-RAY DIFFRACTION	99
2.072-2.0993	0.2482	137	0.1982	2598	X-RAY DIFFRACTION	99
2.0993-2.128	0.2063	137	0.1937	2616	X-RAY DIFFRACTION	99
2.128-2.1584	0.2474	137	0.1933	2594	X-RAY DIFFRACTION	99
2.1584-2.1906	0.2568	137	0.1806	2607	X-RAY DIFFRACTION	99
2.1906-2.2248	0.2257	139	0.1774	2640	X-RAY DIFFRACTION	99
2.2248-2.2613	0.2201	136	0.1785	2591	X-RAY DIFFRACTION	99
2.2613-2.3003	0.2359	138	0.1747	2615	X-RAY DIFFRACTION	99
2.3003-2.3421	0.2333	139	0.1714	2645	X-RAY DIFFRACTION	99
2.3421-2.3871	0.226	139	0.1691	2637	X-RAY DIFFRACTION	99
2.3871-2.4358	0.2125	137	0.1651	2603	X-RAY DIFFRACTION	99
2.4358-2.4887	0.2136	137	0.1719	2611	X-RAY DIFFRACTION	99
2.4887-2.5466	0.2101	139	0.1637	2629	X-RAY DIFFRACTION	99
2.5466-2.6102	0.2125	138	0.1773	2626	X-RAY DIFFRACTION	100
2.6102-2.6808	0.233	140	0.1758	2665	X-RAY DIFFRACTION	99
2.6808-2.7596	0.2171	139	0.1733	2632	X-RAY DIFFRACTION	99
2.7596-2.8486	0.2246	138	0.181	2632	X-RAY DIFFRACTION	100
2.8486-2.9503	0.2133	141	0.1721	2660	X-RAY DIFFRACTION	100
2.9503-3.0683	0.1946	140	0.1687	2660	X-RAY DIFFRACTION	100
3.0683-3.2078	0.2029	138	0.167	2640	X-RAY DIFFRACTION	99
3.2078-3.3767	0.1949	140	0.1678	2651	X-RAY DIFFRACTION	100
3.3767-3.5879	0.1749	142	0.1557	2691	X-RAY DIFFRACTION	100
3.5879-3.8643	0.1946	141	0.1494	2677	X-RAY DIFFRACTION	100
3.8643-4.2521	0.1852	140	0.1467	2669	X-RAY DIFFRACTION	99
4.2521-4.8649	0.1508	142	0.1428	2697	X-RAY DIFFRACTION	99
4.8649-6.1198	0.2272	144	0.1768	2727	X-RAY DIFFRACTION	99
6.1198-29.0191	0.1995	150	0.1933	2851	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	1.119	-0.3519	0.3614	1.4922	-0.7402	1.5785	0.0225	0.0432	-0.113	-0.2249	0.1225	0.1978	0.2099	-0.1618	-0.1156	0.1799	-0.0332	-0.0211	0.163	-0.0047	0.1617	-35.6122	0.3958	-14.7125
2	2.2282	0.0924	0.6841	1.5898	0.3885	2.4088	0.1083	-0.2096	-0.1494	-0.1074	0.0876	0.4776	0.1516	-0.4462	-0.1432	0.1923	-0.0416	-0.0709	0.1914	0.0303	0.244	-43.1082	3.7128	-12.0002
3	0.6296	-0.1417	-0.195	1.2616	-0.3365	0.9341	0.0177	0.0171	0.0373	-0.2335	0.0081	0.018	0.0698	0.0891	-0.0458	0.1998	-0.0091	0.01	0.1508	-0.0059	0.1138	-26.4096	12.6404	-17.0934
4	1.5403	0.5119	0.5386	1.9544	0.4366	3.4685	-0.179	0.3475	0.107	-0.3329	0.1671	0.2334	-0.1903	-0.0542	-0.0542	0.2706	-0.036	-0.002	0.1852	0.0409	0.1619	-33.3397	22.7985	-29.7015
5	0.9336	0.0869	-0.1249	1.5776	0.1172	2.8043	0.0634	-0.0655	0.1477	0.0537	0.0337	-0.1223	-0.6003	0.4284	-0.0859	0.2834	-0.056	0.0268	0.1891	-0.0234	0.1873	-22.7059	32.7351	-8.2574
6	0.7174	-0.1354	-0.0237	1.5609	-0.2942	1.2145	0.0858	0.0117	0.0263	-0.0606	-0.0642	0.0075	0.1025	0.0964	-0.0775	0.1987	-0.0181	0.0007	0.155	-0.0011	0.1367	-25.7445	16.7782	-19.6737
7	0.9124	-0.3008	0.155	1.1371	0.1419	1.686	0.2045	0.1676	0.1884	-0.0201	-0.0295	0.1523	-0.2486	-0.3188	-0.1348	0.2387	-0.0067	0.0403	0.2187	0.0293	0.2069	-38.2673	30.906	-12.6563
8	0.8569	0.4416	0.069	2.77	0.4647	1.5722	0.0832	0.3111	-0.0751	-0.3624	0.1111	0.2163	0.1182	-0.1397	-0.107	0.2822	-0.011	-0.0971	0.2495	0.0483	0.2065	-42.5711	12.6035	-29.3715
9	1.2845	0.3357	0.0266	2.203	-0.6257	1.384	0.0799	-0.0502	0.1079	-0.0185	-0.0047	0.2503	-0.2002	-0.255	-0.0864	0.1916	0.0505	0.0419	0.1965	-0.0221	0.1959	-39.4751	23.9765	7.0926
10	0.6002	0.0362	0.1606	1.3621	-0.0337	0.6702	-0.0087	-0.0045	0.0883	0.0995	0.0582	-0.0384	-0.1414	0.1347	-0.0778	0.1653	-0.0154	0.019	0.1779	-0.0318	0.1304	-25.5185	18.1784	7.4176
11	1.7892	-0.6726	-0.8719	1.9374	1.1329	4.059	-0.193	-0.3103	-0.0864	0.4964	0.1524	-0.0095	0.3201	-0.1271	0.105	0.2336	0.0424	-0.0151	0.2871	-0.0169	0.1263	-24.1398	6.5103	20.7415
12	0.5003	-0.24	-0.2349	1.1886	0.3302	0.9704	0.0844	-0.0582	0.0112	-0.0239	-0.0288	-0.1258	-0.0532	0.1357	-0.0622	0.1372	0.0079	0.0026	0.174	-0.0189	0.1374	-19.3929	5.1135	2.7866
13	1.5343	-1.5031	-1.0273	4.7644	2.9138	4.2286	0.0295	-0.2219	0.0174	0.3876	0.0602	-0.0665	-0.025	0.0251	-0.0123	0.1883	-0.0253	0.0312	0.2064	-0.0033	0.1171	-35.5762	7.1953	17.3977
14	3.2927	-0.8969	-1.6027	3.8116	1.0988	3.9505	-0.0824	-0.1757	0.2167	0.5625	-0.1046	0.2005	0.1346	-0.293	0.1585	0.1529	-0.0141	-0.0196	0.1774	-0.0046	0.2144	-89.9821	-17.6006	16.2412
15	0.7446	-0.1537	0.1315	0.7513	0.0067	0.6061	-0.0243	-0.0596	0.0376	0.0683	0.0311	0.0277	0.0514	-0.0057	-0.0023	0.137	-0.0197	0.0047	0.131	-0.0252	0.1069	-72.2891	-20.216	14.7601
16	1.8804	-0.3135	0.4197	2.1825	-0.9774	2.9884	0.0302	-0.2969	0.0345	0.1777	-0.0688	-0.2766	0.2544	0.1951	0.0099	0.1902	-0.0335	-0.0212	0.2048	-0.031	0.175	-54.2519	-19.0553	20.8228
17	0.6394	0.0587	-0.0763	0.8141	-0.3068	1.1691	0.0371	-0.0194	0.0766	0.0492	-0.0547	-0.0538	-0.0995	0.1227	0.0257	0.0984	-0.0119	-0.0056	0.1352	-0.0193	0.1322	-59.8707	-14.1405	8.961
18	3.4719	1.2315	-0.8348	4.8229	-0.9667	3.4582	-0.1162	0.3712	0.117	-0.4324	-0.0652	-0.4003	-0.1778	0.598	0.1191	0.1878	-0.0337	0.0031	0.2472	0.002	0.218	-57.7847	-12.3746	-11.5083
19	1.6119	0.1799	0.5777	1.1409	-0.1885	1.7152	-0.1077	0.3487	-0.1446	-0.1906	0.0679	-0.0901	0.0331	0.2162	0.0728	0.1751	-0.0099	0.0312	0.1468	-0.0227	0.1544	-67.5512	-19.1936	-18.0527
20	2.2907	0.7232	0.6522	1.8088	0.557	2.7809	-0.0011	0.1119	-0.3538	0.0544	0.0262	-0.0067	0.3631	-0.0177	-0.0809	0.1528	0.0243	0.0327	0.1002	-0.0138	0.1722	-75.9734	-26.6845	-13.0984
21	0.7403	-0.0338	-0.1383	0.7939	0.322	0.8411	0.0297	0.0541	0.0824	-0.1035	-0.0441	-0.0228	-0.0274	-0.0313	0.0247	0.1359	0.0045	0.0028	0.1164	0.0033	0.1294	-77.8071	-12.039	-10.5309
22	2.1253	0.0115	0.2495	0.7626	-0.0204	0.169	0.0424	-0.0642	0.3256	0.1246	-0.1024	0.0357	-0.1212	-0.0013	0.0682	0.2088	0.0046	-0.0026	0.119	-0.014	0.2052	-75.0909	2.3272	-3.1406
23	1.3133	-0.3202	-0.1576	1.1199	0.0203	2.9385	0.0607	0.3131	-0.0054	-0.2455	0.0464	0.4188	0.2025	-0.2679	0.0253	0.1525	0.0397	-0.0566	0.2086	-0.0066	0.2457	-93.2883	-10.2606	-15.2837
24	0.8977	-0.2746	-0.2819	0.4151	-0.5483	2.2833	-0.1357	-0.0828	0.065	0.1667	0.0922	0.0553	-0.3188	-0.0977	0.0261	0.1486	0.0238	-0.0121	0.161	-0.0341	0.1956	-89.3378	-4.424	9.4962
25	3.1823	-0.4515	-1.2843	0.5951	0.6359	1.3237	-0.0923	-0.0888	0.0833	-0.0246	0.0578	-0.0254	0.0095	0.0608	0.0416	0.1258	0.0037	-0.018	0.0991	-0.004	0.1388	-80.1643	-4.9081	-6.6744
26	0.4769	0.1223	-0.1471	0.5606	-0.1032	0.8832	-0.0096	-0.0762	0.0062	-0.0952	-0.0504	0.1314	-0.0012	-0.1061	0.0551	0.1166	0.0105	-0.0144	0.1401	-0.0269	0.1615	-89.6664	-12.3125	-2.223
27	2.224	-0.3914	-1.5503	0.9989	-0.1603	3.791	-0.0367	0.1978	-0.0877	-0.2943	-0.0074	0.0766	0.1723	-0.277	0.0437	0.1747	-0.0307	-0.0239	0.1718	-0.0402	0.1576	-88.3392	-21.1027	-15.8109

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 61 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 62 through 83 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 84 through 166 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 193 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 225 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 226 through 255 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 256 through 277 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 278 through 296 )	A
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 8 through 79 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 166 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 167 through 193 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 194 through 268 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 269 through 295 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 7 through 24 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 25 through 166 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 167 through 193 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 194 through 296 )	C
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 7 through 24 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 25 through 47 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 48 through 83 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 84 through 142 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 143 through 166 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 167 through 193 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 194 through 226 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 227 through 245 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 246 through 268 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 269 through 296 )	D

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