PDB-5cyf: Crystal structure of isoform 2 of uridine phosphorylase from Schi...

ID or keywords:

Entry

Database: PDB / ID: 5cyf

Title

Crystal structure of isoform 2 of uridine phosphorylase from Schistosoma mansoni in complex with citrate

Components

Putative uridine phosphorylase

Keywords

TRANSFERASE

Function / homology

Function and homology information

nucleotide catabolic process / nucleoside metabolic process / catalytic activity / identical protein binding / cytosol
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.983 Å

Authors

Romanello, L. / Torini, J.R. / 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 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2016	Group: Database references
Revision 1.2	Apr 17, 2019	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / 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 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	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	5cyf.cif.gz	351 KB	Display	PDBx/mmCIF format
PDB format	pdb5cyf.ent.gz	286.8 KB	Display	PDB format
PDBx/mmJSON format	5cyf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5cyf_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	5cyf_full_validation.pdf.gz	468.7 KB	Display
Data in XML	5cyf_validation.xml.gz	37.5 KB	Display
Data in CIF	5cyf_validation.cif.gz	54.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyf ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyf	HTTPS FTP

-
Related structure data

Related structure data	4txhC 4txjC 4txlC 4txmC 4txnC 5cygC 3eueS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5cyg-d 7bjv-1 3p0e-2 3nbq-1 4txn-2 4txj-1 4jyg-d 4txh-1 4txj-2 3ku4-2 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
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Putative uridine phosphorylase

B: Putative uridine phosphorylase

C: Putative uridine phosphorylase

hetero molecules

98.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uridine phosphorylase

B: Putative 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: Putative uridine phosphorylase

hetero molecules

C: Putative uridine phosphorylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	112.530, 112.530, 152.351
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	C-429- HOH

#1: Protein	Putative uridine phosphorylase Mass: 32742.711 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_082420 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G4VGH9, uridine phosphorylase
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.83 Å³/Da / Density % sol: 56.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG4000, 20% isopropanol, 100 sodium citrate tribasic pH 5.6 PH range: 5.2-6.0

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: W01B-MX2 / Wavelength: 1.458 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2009

Radiation

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

Radiation wavelength

Wavelength: 1.458 Å / Relative weight: 1

Reflection

Resolution: 1.983→97.454 Å / Num. all: 74612 / Num. obs: 74612 / % possible obs: 96 % / Redundancy: 4.5 % / B_iso Wilson estimate: 28.23 Å² / R_pim(I) all: 0.049 / R_rim(I) all: 0.107 / R_sym value: 0.095 / Net I/av σ(I): 5.652 / Net I/σ(I): 9.7 / Num. measured all: 338455

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.98-2.09	4.6	0.598	1.3	46298	10159	0.307	0.598	2.4	90.4
2.09-2.22	4.5	0.403	1.9	43963	9782	0.207	0.403	3.5	92
2.22-2.37	4.4	0.316	2.2	41736	9447	0.163	0.316	4.8	94.3
2.37-2.56	4.4	0.191	3.9	39406	9026	0.1	0.191	6.5	96.4
2.56-2.8	4.4	0.13	5.6	37225	8447	0.068	0.13	8.8	98.4
2.8-3.14	4.5	0.088	8	34869	7728	0.046	0.088	12.1	99.2
3.14-3.62	4.7	0.083	7.1	32218	6907	0.042	0.083	16.5	99.5
3.62-4.43	4.8	0.073	8.3	28382	5885	0.036	0.073	20.6	100
4.43-6.27	4.8	0.053	10.3	22388	4631	0.027	0.053	22.1	100
6.27-31.77	4.6	0.04	14.5	11970	2600	0.021	0.04	22.6	98.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
SCALA	3.3.9	data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EUE

3eue

Resolution: 1.983→31.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2102	3768	5.05 %	Random selection
R_work	0.1689	-	-	-
obs	0.1709	74564	95.94 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.983→31.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6594	0	26	587	7207

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6785
X-RAY DIFFRACTION	f_angle_d	1.245	9172
X-RAY DIFFRACTION	f_dihedral_angle_d	13.535	2456
X-RAY DIFFRACTION	f_chiral_restr	0.056	1062
X-RAY DIFFRACTION	f_plane_restr	0.006	1173

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 (%)
1.983-2.0081	0.2631	129	0.234	2417	X-RAY DIFFRACTION	89
2.0081-2.0345	0.267	136	0.2254	2433	X-RAY DIFFRACTION	91
2.0345-2.0624	0.2726	136	0.2083	2449	X-RAY DIFFRACTION	91
2.0624-2.0918	0.2775	136	0.2138	2443	X-RAY DIFFRACTION	91
2.0918-2.1231	0.262	140	0.2039	2490	X-RAY DIFFRACTION	91
2.1231-2.1562	0.2503	132	0.1961	2486	X-RAY DIFFRACTION	93
2.1562-2.1916	0.2337	119	0.197	2483	X-RAY DIFFRACTION	92
2.1916-2.2294	0.2523	136	0.203	2554	X-RAY DIFFRACTION	93
2.2294-2.2699	0.3206	135	0.2435	2499	X-RAY DIFFRACTION	93
2.2699-2.3135	0.2213	129	0.187	2540	X-RAY DIFFRACTION	94
2.3135-2.3607	0.2417	129	0.1868	2577	X-RAY DIFFRACTION	95
2.3607-2.412	0.215	161	0.1712	2560	X-RAY DIFFRACTION	96
2.412-2.4681	0.2046	132	0.1701	2634	X-RAY DIFFRACTION	96
2.4681-2.5298	0.2334	148	0.1698	2630	X-RAY DIFFRACTION	97
2.5298-2.5982	0.2103	143	0.1673	2680	X-RAY DIFFRACTION	98
2.5982-2.6746	0.2241	129	0.1761	2666	X-RAY DIFFRACTION	98
2.6746-2.7609	0.2109	150	0.1717	2659	X-RAY DIFFRACTION	98
2.7609-2.8595	0.2025	158	0.1736	2686	X-RAY DIFFRACTION	99
2.8595-2.9739	0.2377	130	0.1752	2703	X-RAY DIFFRACTION	99
2.9739-3.1092	0.2382	160	0.1789	2697	X-RAY DIFFRACTION	99
3.1092-3.2729	0.2091	150	0.1748	2739	X-RAY DIFFRACTION	99
3.2729-3.4778	0.2248	129	0.1605	2728	X-RAY DIFFRACTION	100
3.4778-3.7459	0.1792	158	0.1562	2752	X-RAY DIFFRACTION	100
3.7459-4.1221	0.1654	136	0.14	2790	X-RAY DIFFRACTION	100
4.1221-4.717	0.1544	149	0.1308	2773	X-RAY DIFFRACTION	100
4.717-5.9365	0.1947	134	0.1522	2820	X-RAY DIFFRACTION	100
5.9365-31.7745	0.2024	144	0.1704	2908	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	4.3436	2.2542	-0.6263	3.6922	0.1291	0.9278	-0.0107	0.1758	0.7099	-0.0401	0.106	-0.0739	-0.3461	0.1011	-0.0904	0.3955	0.0426	0.0033	0.2209	0.0746	0.372	-54.4365	23.5901	7.8209
2	1.6326	-0.2734	-0.585	0.7857	0.8936	1.6388	0.001	0.042	0.1251	0.1393	0.0024	0.1858	-0.1631	-0.1372	0.0166	0.2428	0.072	-0.0062	0.2048	0.014	0.2844	-66.9863	18.0515	21.126
3	1.4595	-0.4482	-0.1177	0.8953	0.291	0.743	-0.0187	0.0135	0.0874	0.0744	0.0314	0.057	-0.1226	-0.1221	-0.0158	0.2235	0.0356	-0.0008	0.1579	0.0064	0.1842	-60.0269	12.37	22.2509
4	1.3488	-0.1036	-0.1437	1.9157	-0.3441	2.143	-0.0455	-0.3563	0.0164	0.3338	0.0655	-0.0474	-0.1704	0.2005	-0.0373	0.2484	0.0425	-0.0534	0.1721	-0.0123	0.2044	-48.6076	8.7485	30.276
5	0.9444	-0.4105	-0.0111	1.4871	-0.1286	1.1382	-0.0547	-0.1541	-0.1105	0.147	0.0909	-0.2454	0.1452	0.0906	-0.0369	0.2099	0.0367	-0.0292	0.1671	0.0141	0.2122	-46.9179	-4.0284	25.3124
6	2.4205	-0.9857	0.6417	1.9017	-0.7489	2.3331	0.0508	-0.1504	-0.5433	0.0068	0.1412	0.3323	0.3485	-0.2154	-0.1302	0.2758	0.0186	-0.0215	0.2092	0.0311	0.2719	-55.8433	-1.6176	30.3965
7	2.7462	-1.2425	1.1396	2.1401	-0.9317	2.2846	-0.0332	-0.4807	-0.5654	0.0804	0.1579	0.8856	0.044	-0.5728	-0.007	0.2759	0.0604	0.0104	0.3056	0.0333	0.3481	-67.7913	8.7341	33.8517
8	2.7712	-1.2048	1.1257	2.6484	-0.0089	0.6614	0.1926	-0.3191	-0.5351	0.1876	0.0466	-0.1883	0.7294	0.011	-0.1442	0.47	0.0172	-0.0771	0.244	0.0627	0.3197	-56.4989	-18.0111	18.7134
9	1.1081	0.6902	-0.5775	0.7574	0.1671	1.4486	-0.0031	0.0525	-0.2454	-0.0869	0.0703	0.1529	0.4445	-0.3251	-0.0511	0.3453	-0.1069	-0.0607	0.2353	0.0331	0.2628	-63.8922	-17.1561	7.1958
10	0.0298	-0.0765	-0.0155	1.4305	0.8087	0.4614	-0.2416	0.077	0.2094	-0.6956	0.1969	0.5714	-0.1469	-0.2827	-0.0076	0.4054	-0.0835	-0.1535	0.3419	0.0713	0.3517	-71.5998	-7.7089	-1.235
11	1.0516	0.748	0.3166	1.8209	-0.1997	1.1263	-0.0423	0.0596	-0.0856	-0.2272	0.0922	-0.0079	0.1206	-0.1176	-0.0456	0.235	-0.0078	-0.0159	0.1514	-0.0034	0.1904	-55.5013	-5.7631	3.5967
12	1.5898	0.4648	0.2928	1.9561	-0.3916	3.1025	-0.1928	0.4207	-0.1813	-0.4137	0.1226	-0.3083	0.1525	0.5833	0.0029	0.3443	0.0038	0.0929	0.1907	-0.0568	0.3035	-45.0907	-7.0569	-0.3843
13	0.9961	0.6426	0.1145	2.6381	-0.0383	1.1132	-0.1408	0.2397	0.0092	-0.2554	0.1617	-0.1645	-0.0004	0.1069	0.0087	0.2265	-0.0274	0.0278	0.1873	0.0129	0.171	-45.9247	7.8161	0.4075
14	2.2142	0.3765	-0.2622	0.1505	0.3491	1.7454	-0.1684	0.3558	0.4907	-0.2438	0.2707	0.3361	-0.3293	0.0468	0.0071	0.2498	-0.0375	0.0137	0.1862	0.0093	0.2206	-51.9135	6.3003	-4.0176
15	2.5239	0.5126	-0.4181	1.2913	0.0271	0.5542	-0.0315	0.6602	0.5184	-0.3151	-0.0032	0.724	0.4217	-0.7573	-0.0502	0.4652	-0.1963	-0.1436	0.4246	0.0085	0.2518	-63.8255	-3.5141	-9.5482
16	3.3461	-0.5156	0.5926	2.1396	-1.1252	1.2043	-0.3151	-0.3142	-0.614	0.3022	0.3626	0.59	0.0911	-0.3939	-0.1009	0.395	0.0132	0.0726	0.3565	0.1115	0.4177	-103.4462	4.986	14.8121
17	1.795	-0.4336	0.1277	1.4599	-0.1918	0.8994	-0.1144	0.0424	0.1089	0.1293	0.0686	-0.1319	0.0985	-0.0558	0.0359	0.2515	0.0275	-0.0395	0.2151	0.0108	0.2135	-88.8695	15.636	3.2814
18	2.6228	-0.2345	-0.6865	2.0098	-1.3853	1.2047	-0.2552	0.1364	-0.6319	-0.3115	0.1494	-0.0053	0.752	-0.3124	0.0348	0.4703	-0.0111	-0.0021	0.2499	0.0117	0.347	-88.1045	2.0285	3.0222

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 142 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 143 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 268 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 269 through 296 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 47 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 48 through 71 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 148 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 149 through 179 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 180 through 245 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 246 through 268 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 269 through 296 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 9 through 83 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 84 through 245 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 246 through 296 )

-
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