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

ID or keywords:

Entry

Database: PDB / ID: 4txl

Title

Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with uracil

Components

Uridine phosphorylase

Keywords

TRANSFERASE / Uridine phosphorylase

Function / homology

Function and homology information

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

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.92 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	Jul 15, 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 / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 2.0	Apr 17, 2019	Group: Author supporting evidence / Data collection / Polymer sequence Category: entity_poly / pdbx_audit_support Item: _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2	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

-
Download

PDBx/mmCIF format	4txl.cif.gz	458 KB	Display	PDBx/mmCIF format
PDB format	pdb4txl.ent.gz	378 KB	Display	PDB format
PDBx/mmJSON format	4txl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/4txl ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txl	HTTPS FTP

-
Related structure data

Related structure data	4txhC 4txjSC 4txmC 4txnC 5cyfC 5cygC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3whs-d 3nbq-1 4y23-d 5dxm-d 3a75-2 4zf6-d 4txj-1 3whr-d 1bu7-1 6dwn-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: Uridine phosphorylase

D: Uridine phosphorylase

A: Uridine phosphorylase

B: Uridine phosphorylase

hetero molecules

131 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
65.7 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
65.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.850, 108.530, 118.670
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
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-URA / URACIL Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₄N₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1139 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.95 %
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

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9611 Å / Relative weight: 1
Reflection	Resolution: 1.92→95.85 Å / Num. obs: 94695 / % possible obs: 99.7 % / Redundancy: 3.9 % / R_merge(I) obs: 0.076 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.92→1.97 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.9_1692)	refinement
XDS		data reduction
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
GDA		data collection
xia2		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4TXJ

4txj

Resolution: 1.92→71.84 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	4744	5.01 %	Random selection
R_work	0.191	-	-	-
obs	0.192	94623	99.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→71.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8530	0	52	1139	9721

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8767
X-RAY DIFFRACTION	f_angle_d	0.86	11879
X-RAY DIFFRACTION	f_dihedral_angle_d	12.318	3028
X-RAY DIFFRACTION	f_chiral_restr	0.031	1385
X-RAY DIFFRACTION	f_plane_restr	0.003	1530

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 (%)
1.92-1.9418	0.2733	153	0.2617	2956	X-RAY DIFFRACTION	100
1.9418-1.9647	0.2537	132	0.2501	2996	X-RAY DIFFRACTION	100
1.9647-1.9886	0.2859	151	0.2443	2971	X-RAY DIFFRACTION	100
1.9886-2.0138	0.2997	154	0.247	2994	X-RAY DIFFRACTION	100
2.0138-2.0403	0.2732	159	0.2337	2968	X-RAY DIFFRACTION	100
2.0403-2.0683	0.2677	156	0.2293	2943	X-RAY DIFFRACTION	100
2.0683-2.0978	0.2317	173	0.2215	2975	X-RAY DIFFRACTION	100
2.0978-2.1291	0.2238	143	0.2132	3012	X-RAY DIFFRACTION	100
2.1291-2.1624	0.2439	157	0.2169	2941	X-RAY DIFFRACTION	100
2.1624-2.1979	0.2556	160	0.2065	2987	X-RAY DIFFRACTION	100
2.1979-2.2358	0.2386	155	0.2038	3002	X-RAY DIFFRACTION	100
2.2358-2.2764	0.2399	175	0.2017	2954	X-RAY DIFFRACTION	100
2.2764-2.3202	0.239	157	0.2021	2958	X-RAY DIFFRACTION	100
2.3202-2.3676	0.2646	157	0.2034	2998	X-RAY DIFFRACTION	100
2.3676-2.419	0.2209	166	0.1977	2975	X-RAY DIFFRACTION	100
2.419-2.4753	0.2256	151	0.1942	3004	X-RAY DIFFRACTION	100
2.4753-2.5372	0.2165	178	0.1887	2962	X-RAY DIFFRACTION	100
2.5372-2.6058	0.2401	149	0.1966	3001	X-RAY DIFFRACTION	100
2.6058-2.6825	0.2358	130	0.1937	3031	X-RAY DIFFRACTION	100
2.6825-2.7691	0.2418	170	0.2001	2966	X-RAY DIFFRACTION	100
2.7691-2.8681	0.2791	153	0.197	3003	X-RAY DIFFRACTION	100
2.8681-2.9829	0.2455	167	0.1886	2998	X-RAY DIFFRACTION	100
2.9829-3.1187	0.2197	140	0.1851	3009	X-RAY DIFFRACTION	100
3.1187-3.2831	0.2256	162	0.1911	3000	X-RAY DIFFRACTION	99
3.2831-3.4888	0.209	149	0.1726	2980	X-RAY DIFFRACTION	98
3.4888-3.7581	0.1932	156	0.1616	2982	X-RAY DIFFRACTION	99
3.7581-4.1363	0.1748	164	0.159	3024	X-RAY DIFFRACTION	99
4.1363-4.7347	0.161	185	0.1492	3024	X-RAY DIFFRACTION	99
4.7347-5.9648	0.2019	169	0.1824	3075	X-RAY DIFFRACTION	99
5.9648-71.89	0.2111	173	0.1991	3190	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	1.1679	-0.1101	0.2951	1.1679	-0.1918	1.0451	0.0209	-0.1193	0.0608	0.1299	-0.0205	0.1623	0.0242	-0.1243	-0.0079	0.1081	-0.025	0.0135	0.1449	-0.0353	0.1249	-24.7914	-20.6819	15.2864
2	2.6569	-0.572	0.0593	2.8367	-0.7144	2.3184	-0.0612	-0.2629	-0.0671	0.254	0.0113	-0.4356	0.1063	0.3506	0.0304	0.1455	-0.0318	-0.0672	0.2052	-0.0183	0.2183	-4.4972	-20.0147	21.3789
3	1.0205	0.3181	-0.1473	1.0255	-0.2703	1.4146	-0.0027	-0.0063	0.1634	0.1035	-0.0329	-0.1117	-0.0388	0.0989	0.0182	0.0795	-0.0104	-0.0236	0.1275	-0.0159	0.1726	-9.7884	-14.8718	9.441
4	3.0941	0.1643	-0.279	2.7193	-0.8826	2.2105	-0.1228	0.3079	0.1737	-0.1986	-0.1311	-0.5382	-0.1818	0.4525	0.1836	0.1662	-0.0197	-0.0021	0.2632	0.0478	0.234	-7.2749	-13.0755	-10.4985
5	2.7414	0.3221	0.0698	1.2808	-0.2582	1.6621	-0.0651	0.5002	-0.3313	-0.2517	0.0503	-0.0534	0.1742	0.0293	0.0164	0.1689	-0.0037	-0.0089	0.1861	-0.039	0.1682	-23.558	-23.5457	-16.1943
6	1.8712	0.3846	0.0683	1.0396	0.2248	1.2967	-0.0565	0.1078	0.2349	-0.0433	0.0064	0.0183	-0.0537	0.0244	0.0532	0.0932	-0.0051	-0.0215	0.1145	0.0332	0.1644	-25.654	-10.0026	-7.9441
7	1.6917	-0.371	0.1542	1.3683	0.01	4.0519	0.0041	0.2383	0.1527	-0.3944	-0.0411	0.3763	-0.0235	-0.5737	0.0087	0.1698	0.0293	-0.0853	0.2867	0.039	0.3622	-42.8781	-9.4322	-15.4679
8	1.0369	-0.0395	0.5157	1.2172	-0.8122	2.8832	0.0245	-0.2734	0.2402	0.2416	0.0264	0.1818	-0.2408	-0.2753	0.0063	0.1356	0.0211	0.0242	0.207	-0.0624	0.2694	-35.7812	-8.4448	12.3483
9	2.3032	-0.899	-0.3479	1.2118	0.3383	2.2768	-0.0888	-0.1353	0.3038	0.0039	0.0062	0.278	-0.2676	-0.1738	0.0372	0.1263	0.0236	-0.0281	0.14	-0.0223	0.325	-36.202	-2.7032	-0.7805
10	0.9052	0.262	0.2542	0.9712	-0.4335	1.6132	-0.0215	0.0177	0.2149	-0.013	0.0213	0.2571	-0.0026	-0.3273	-0.0091	0.0901	0.0022	-0.0257	0.1743	0.0077	0.242	-39.8422	-12.3179	-1.9093
11	3.0768	0.2549	-0.9964	1.8189	-0.6363	4.9024	-0.1132	0.4805	-0.1425	-0.3429	0.0365	0.1436	0.0834	-0.2146	0.0915	0.1466	-0.0365	-0.05	0.2299	-0.0426	0.2113	-38.2337	-20.909	-15.8725
12	2.5621	2.8738	1.2027	7.0558	1.1925	0.5725	-0.0593	-0.242	0.8389	-0.2906	0.2402	-0.2201	-0.6105	0.0945	-0.1887	1.0242	0.1854	0.1536	0.3884	-0.1541	0.5883	16.4708	34.5303	0.5854
13	0.7095	-0.6249	-0.3652	0.9342	0.8331	0.9435	-0.1105	-0.4064	0.2352	-0.0774	0.1628	-0.0201	-0.9242	-0.6092	-0.0723	0.5431	0.2788	0.042	0.4621	-0.1568	0.1786	13.4829	20.8633	9.5475
14	0.65	-0.1545	-0.2205	1.5092	0.3772	1.9159	-0.0443	-0.3519	0.351	-0.0047	0.6068	-0.777	-0.276	0.82	-0.2817	0.3346	-0.0146	-0.0178	0.5934	-0.3065	0.5194	32.4569	13.4215	9.0054
15	0.1594	-0.3479	-0.2016	1.2708	0.4729	0.9016	-0.0032	-0.2994	0.181	0.1087	0.5642	-0.8217	-0.0485	0.6598	-0.3281	0.2084	0.0443	0.0107	0.4613	-0.2423	0.4211	30.331	4.6683	3.3628
16	0.4084	-0.2286	-0.5719	2.6976	3.9484	6.1915	-0.1329	-0.1731	-0.0734	0.4709	-0.0425	0.2352	0.2585	-0.4975	0.1899	0.3832	0.1335	0.0018	0.421	-0.0207	0.1515	15.6245	7.3353	18.0986
17	1.3457	-0.0692	0.7816	2.0806	-0.4674	2.6068	0.1169	0.1208	-0.1216	-0.6062	-0.1518	0.2554	-0.2943	-0.7907	0.0188	0.3658	0.0859	-0.0154	0.3744	-0.0635	0.1753	12.7812	2.3051	-13.5944
18	0.3214	-0.3929	-0.3042	0.722	0.5084	0.5185	0.1518	0.2803	0.5259	-0.9314	0.0685	-0.2576	-1.01	-0.0272	-0.1183	1.4364	0.023	0.3495	0.2834	-0.0673	0.3481	20.5778	21.7495	-18.4485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'C' AND (RESID 7 THROUGH 166 )
2	X-RAY DIFFRACTION	2	CHAIN 'C' AND (RESID 167 THROUGH 193 )
3	X-RAY DIFFRACTION	3	CHAIN 'C' AND (RESID 194 THROUGH 296 )
4	X-RAY DIFFRACTION	4	CHAIN 'D' AND (RESID 8 THROUGH 24 )
5	X-RAY DIFFRACTION	5	CHAIN 'D' AND (RESID 25 THROUGH 71 )
6	X-RAY DIFFRACTION	6	CHAIN 'D' AND (RESID 72 THROUGH 166 )
7	X-RAY DIFFRACTION	7	CHAIN 'D' AND (RESID 167 THROUGH 193 )
8	X-RAY DIFFRACTION	8	CHAIN 'D' AND (RESID 194 THROUGH 212 )
9	X-RAY DIFFRACTION	9	CHAIN 'D' AND (RESID 213 THROUGH 245 )
10	X-RAY DIFFRACTION	10	CHAIN 'D' AND (RESID 246 THROUGH 268 )
11	X-RAY DIFFRACTION	11	CHAIN 'D' AND (RESID 269 THROUGH 296 )
12	X-RAY DIFFRACTION	12	CHAIN 'A' AND (RESID 8 THROUGH 24 )
13	X-RAY DIFFRACTION	13	CHAIN 'A' AND (RESID 25 THROUGH 125 )
14	X-RAY DIFFRACTION	14	CHAIN 'A' AND (RESID 126 THROUGH 176 )
15	X-RAY DIFFRACTION	15	CHAIN 'A' AND (RESID 177 THROUGH 268 )
16	X-RAY DIFFRACTION	16	CHAIN 'A' AND (RESID 269 THROUGH 295 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 8 THROUGH 111 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 112 THROUGH 294 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi