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

ID or keywords:

Entry

Database: PDB / ID: 4txh

Title

Crystal structure of uridine phosphorylase from Schistosoma mansoni in APO form

Components

Uridine phosphorylase

Keywords

TRANSFERASE / Uridine phosphorylase

Function / homology

Function and homology information

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

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.892 Å

Authors

Torini, J. / Romanello, L. / Marinho, A. / Brandao-Neto, J. / Cassago, A. / DeMarco, R. / 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 / 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.name
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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Download

PDBx/mmCIF format	4txh.cif.gz	456 KB	Display	PDBx/mmCIF format
PDB format	pdb4txh.ent.gz	374.7 KB	Display	PDB format
PDBx/mmJSON format	4txh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4txh_validation.pdf.gz	461.2 KB	Display	wwPDB validaton report
Full document	4txh_full_validation.pdf.gz	477.4 KB	Display
Data in XML	4txh_validation.xml.gz	48.5 KB	Display
Data in CIF	4txh_validation.cif.gz	70.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/4txh ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txh	HTTPS FTP

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Related structure data

Related structure data	4txjSC 4txlC 4txmC 4txnC 5cyfC 5cygC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4txn-2 3nbq-1 4txj-1 5cyg-d 4txn-1 5cyf-1 4txl-2 4txl-1 4iw6-d 3h5u-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

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

2

C: Uridine phosphorylase

D: Uridine phosphorylase

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

Unit cell

Length a, b, c (Å)	96.070, 109.030, 119.040
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) / Strain: BH / Gene: Smp_082430, UP1 / 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.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.39 Å³/Da / Density % sol: 48.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM Bis-Tris pH 5.5. 20-25% PEG3350

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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: Nov 25, 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: 1.89→96.07 Å / Num. obs: 100065 / % possible obs: 99.9 % / Redundancy: 4.4 % / R_merge(I) obs: 0.077 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	Rejects	% possible all
1.89-1.94	4.5	0.546	2.3	1	0	100
8.46-96.07	4	0.057		1	0	98.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
GDA		data collection
xia2		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4TXJ

4txj

Resolution: 1.892→80.402 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2386	4997	5 %	Random selection
R_work	0.2146	94987	-	-
obs	0.2158	99984	99.86 %	-

Solvent computation

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

Displacement parameters

B_iso max: 133 Å² / B_iso mean: 43.805 Å² / B_iso min: 13.17 Å²

Refinement step

Cycle: final / Resolution: 1.892→80.402 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8519	0	10	777	9306
B_iso mean	-	-	22.75	42.67	-
Num. residues	-	-	-	-	1145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8735
X-RAY DIFFRACTION	f_angle_d	0.826	11831
X-RAY DIFFRACTION	f_chiral_restr	0.031	1382
X-RAY DIFFRACTION	f_plane_restr	0.003	1532
X-RAY DIFFRACTION	f_dihedral_angle_d	12.663	3045

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 (%)
1.8923-1.9138	0.3213	156	0.2877	3157	X-RAY DIFFRACTION	100
1.9138-1.9363	0.2844	164	0.2711	3116	X-RAY DIFFRACTION	100
1.9363-1.9599	0.283	151	0.265	3149	X-RAY DIFFRACTION	100
1.9599-1.9848	0.2893	160	0.2643	3131	X-RAY DIFFRACTION	100
1.9848-2.0109	0.2874	175	0.2597	3112	X-RAY DIFFRACTION	100
2.0109-2.0384	0.2683	172	0.2666	3144	X-RAY DIFFRACTION	100
2.0384-2.0675	0.3021	184	0.263	3120	X-RAY DIFFRACTION	100
2.0675-2.0984	0.304	173	0.2525	3120	X-RAY DIFFRACTION	100
2.0984-2.1312	0.2722	158	0.2467	3159	X-RAY DIFFRACTION	100
2.1312-2.1661	0.2823	162	0.2411	3136	X-RAY DIFFRACTION	100
2.1661-2.2035	0.2822	168	0.2434	3144	X-RAY DIFFRACTION	100
2.2035-2.2436	0.2772	169	0.2387	3157	X-RAY DIFFRACTION	100
2.2436-2.2867	0.2569	162	0.2304	3123	X-RAY DIFFRACTION	100
2.2867-2.3334	0.2483	155	0.2352	3151	X-RAY DIFFRACTION	100
2.3334-2.3841	0.2365	173	0.2322	3164	X-RAY DIFFRACTION	100
2.3841-2.4396	0.2843	159	0.2244	3140	X-RAY DIFFRACTION	100
2.4396-2.5006	0.2638	160	0.2316	3160	X-RAY DIFFRACTION	100
2.5006-2.5682	0.252	159	0.2289	3155	X-RAY DIFFRACTION	100
2.5682-2.6438	0.2725	191	0.2253	3167	X-RAY DIFFRACTION	100
2.6438-2.7292	0.2732	160	0.2317	3155	X-RAY DIFFRACTION	100
2.7292-2.8267	0.2553	189	0.2233	3117	X-RAY DIFFRACTION	100
2.8267-2.9399	0.227	159	0.2165	3176	X-RAY DIFFRACTION	100
2.9399-3.0737	0.2642	171	0.2201	3155	X-RAY DIFFRACTION	100
3.0737-3.2357	0.2701	156	0.2175	3203	X-RAY DIFFRACTION	100
3.2357-3.4385	0.2297	157	0.2013	3197	X-RAY DIFFRACTION	100
3.4385-3.704	0.2237	158	0.1912	3202	X-RAY DIFFRACTION	100
3.704-4.0767	0.1845	176	0.1776	3192	X-RAY DIFFRACTION	100
4.0767-4.6665	0.1912	171	0.1674	3235	X-RAY DIFFRACTION	100
4.6665-5.8791	0.2054	169	0.1919	3270	X-RAY DIFFRACTION	100
5.8791-80.4748	0.2142	180	0.2135	3380	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	3.2046	-0.5207	-1.7586	2.9314	1.5982	3.964	-0.0874	-0.3883	0.1265	0.4253	-0.0229	0.538	-0.0715	-0.5547	0.0692	0.2607	-0.0061	0.0572	0.4283	-0.0295	0.334	-40.5789	-18.368	16.1704
2	3.0501	-0.3943	1.0349	1.1146	-0.0337	1.4277	0.1158	-0.3847	-0.2656	0.2452	-0.0327	0.2448	0.3257	-0.3452	-0.0972	0.2353	-0.0842	0.0398	0.2694	0.0016	0.2416	-30.8739	-28.0242	19.1666
3	0.9727	-0.6962	0.6544	2.8312	-1.1738	2.4866	0.1555	0.0797	-0.1713	0.0517	-0.0298	-0.0722	0.4287	0.0895	-0.0992	0.2752	-0.0429	-0.0009	0.2331	-0.0575	0.2011	-19.607	-35.3989	13.0783
4	1.2932	0.0433	0.1262	1.4025	-0.2436	1.4717	0.0393	-0.082	0.0937	0.1189	-0.0475	0.1454	0.1151	-0.0804	0.0065	0.1574	-0.0361	0.0276	0.1792	-0.034	0.1455	-21.5572	-20.6544	14.4716
5	3.1736	-0.2102	1.0933	0.0733	-0.0171	0.4462	-0.1378	-0.1511	0.6888	0.1001	-0.0085	0.0185	-0.2202	-0.0922	0.1698	0.2605	-0.0054	0.014	0.2098	-0.0946	0.3391	-21.8786	-2.3022	15.5613
6	3.1949	-1.7208	0.0224	3.7151	-0.4876	2.321	-0.0439	-0.2601	-0.0082	0.3219	0.0094	-0.3514	0.2549	0.3328	0.0051	0.2203	-0.055	-0.0532	0.2687	-0.0224	0.2534	-4.3146	-20.1562	21.2679
7	0.5678	-0.181	0.8259	1.0652	0.1723	3.3515	0.0324	0.1568	0.1933	-0.0702	0.0482	-0.213	-0.3094	0.3975	-0.0786	0.1777	-0.0567	0.028	0.2622	0.0224	0.3702	-7.0528	-3.8482	0.2968
8	6.1074	1.6263	-0.7751	2.1022	-0.7163	1.7862	0.0774	-0.1874	0.4248	0.2227	-0.0785	0.0604	-0.1476	0.0176	-0.0029	0.1925	-0.02	0.0228	0.1623	-0.0381	0.2319	-16.1671	-10.3368	15.3388
9	1.3794	-0.0681	-0.0507	1.7986	0.2351	2.0215	0.0961	0.0651	0.1998	0.0501	-0.1365	-0.2412	-0.0686	0.3103	0.0541	0.1173	-0.0092	-0.0073	0.2272	0.0142	0.2222	-7.546	-16.1357	7.9968
10	1.9917	0.5168	-0.5767	2.0784	-0.5517	2.6742	0.0176	-0.0094	-0.0945	0.2319	-0.1397	-0.2324	0.2884	0.1191	0.1003	0.2115	-0.0181	-0.0254	0.1945	-0.0137	0.1884	-10.0781	-30.0815	16.6557
11	4.6551	2.2528	-2.3175	5.8854	-1.0134	3.9292	-0.1183	0.3734	0.1856	-0.6364	-0.0731	-0.6812	-0.2142	0.4435	0.1758	0.2807	-0.0082	0.0553	0.3569	0.0637	0.3169	-7.4199	-12.5631	-11.146
12	3.8124	-0.5533	0.5104	2.0421	-0.6129	3.0889	-0.0621	0.7098	-0.1505	-0.5321	-0.0789	-0.1535	0.1549	0.2715	0.1111	0.2799	0.005	0.0466	0.2515	-0.0058	0.1774	-17.0738	-19.4716	-17.8623
13	2.6835	-0.429	-0.4974	1.015	-0.7602	2.0267	0.0413	0.4822	-0.7158	-0.4927	-0.0147	0.0965	0.7321	-0.128	-0.0434	0.3685	0.0047	-0.0332	0.2887	-0.0734	0.3345	-29.4325	-28.2253	-15.2656
14	1.8094	0.1647	0.0796	1.4781	0.0703	1.5717	-0.0304	0.1274	0.2072	-0.1794	-0.0042	0.0938	-0.0415	0.0137	0.0424	0.1599	-0.0041	0.0047	0.1648	0.0226	0.1918	-25.7411	-10.1568	-8.0774
15	2.2897	0.4125	0.1754	1.9087	-0.0502	2.3869	-0.0885	0.3404	0.1358	-0.4829	0.0411	0.4783	0.0392	-0.492	0.0348	0.2885	0.031	-0.0908	0.3776	0.0289	0.4033	-43.1487	-9.9164	-15.47
16	1.0283	-0.6148	0.7345	1.4458	-1.2038	2.7486	-0.0606	-0.3762	0.2228	0.2465	0.1204	0.4586	-0.3565	-0.5316	-0.076	0.1676	0.0322	0.0587	0.3042	-0.0818	0.4404	-39.7569	-4.829	9.9778
17	2.181	0.6205	-0.1578	1.7285	-0.4778	1.9474	-0.0002	0.1712	0.1177	-0.3236	-0.0271	0.2296	0.0318	-0.1626	0.0415	0.1577	0.0316	-0.0435	0.1933	0.0042	0.234	-36.4162	-14.1606	-9.0458
18	0.9002	-0.5464	0.1384	1.5009	0.9403	1.396	-0.1518	-0.3296	0.3578	-0.0818	0.2182	0.1564	-0.9148	-0.4744	0.0036	0.6595	0.3097	0.0353	0.6413	-0.1244	0.3413	10.997	23.6837	8.573
19	1.0161	-0.2636	0.0671	1.5918	-0.1271	1.504	-0.0347	-0.5019	0.5577	0.0154	0.7911	-1.1325	-0.7166	0.5919	-0.2915	0.6206	0.0145	0.1249	0.4857	-0.3671	0.5827	25.0722	18.2267	6.7713
20	0.0983	0.146	0.1794	1.5575	0.651	1.1515	-0.0953	-0.5249	0.3387	0.2819	0.7791	-1.3612	0.0026	0.9846	-0.3996	0.396	0.1023	-0.0531	0.7457	-0.4943	0.6702	29.7868	5.7218	6.7395
21	0.4414	0.2397	-0.2437	2.9078	2.5071	4.5343	-0.2222	-0.1266	-0.0273	0.3877	0.2533	-0.0063	0.0731	-0.1727	-0.0091	0.5562	0.2252	0.0033	0.5374	-0.0403	0.1913	15.581	7.7307	18.4071
22	1.1376	0.3321	0.7353	1.8401	-0.4535	2.5636	0.1919	0.2629	-0.1007	-0.9023	-0.1632	0.3373	-0.4256	-0.7788	-0.0018	0.6457	0.1056	-0.0509	0.5023	-0.067	0.2444	11.6121	2.2055	-13.4881
23	0.4064	-0.3872	-0.2696	0.7322	0.6776	0.8963	0.3235	0.4268	0.7781	-1.2167	0.0517	-0.6204	-1.149	0.3234	-0.2517	1.7782	-0.0797	0.6805	0.2748	-0.045	0.5678	23.8722	19.8795	-16.9657
24	0.6496	-0.563	-0.3783	1.5715	0.8333	0.4741	0.2746	0.0714	0.2986	-1.0761	-0.0929	0.0155	-0.723	-0.3338	-0.0414	1.706	0.1022	0.2142	0.4868	-0.036	0.4971	12.9145	20.3212	-19.8514

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 24 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 47 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 71 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 142 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 143 through 166 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 167 through 193 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 194 through 225 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 226 through 245 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 246 through 268 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 269 through 296 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 7 through 24 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 25 through 47 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 48 through 71 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 72 through 166 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 167 through 193 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 194 through 226 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 227 through 296 )	B
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 8 through 83 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 84 through 162 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 163 through 268 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 269 through 295 )	C
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 8 through 94 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 95 through 241 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 242 through 294 )	D

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi