PDB-5ko5: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase...

ID or keywords:

Entry

Database: PDB / ID: 5ko5

Title

Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with cytosine

Components

Purine nucleoside phosphorylase

Keywords

TRANSFERASE

Function / homology

Function and homology information

nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.36 Å

Authors

Torini, J.R. / Romanello, L. / Bird, L. / Owens, R. / Brandao-Neto, J. / Pereira, H.M.

Funding support

Brazil, 2items

Citation

Journal: PLoS ONE / Year: 2018
Title: The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.
Authors: Torini, J.R. / Romanello, L. / Batista, F.A.H. / Serrao, V.H.B. / Faheem, M. / Zeraik, A.E. / Bird, L. / Nettleship, J. / Reddivari, Y. / Owens, R. / DeMarco, R. / Borges, J.C. / Brandao-Neto, J. / Pereira, H.D.

History

Deposition	Jun 29, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Sep 26, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	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	5ko5.cif.gz	134.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ko5.ent.gz	103 KB	Display	PDB format
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Validation report

Summary document	5ko5_validation.pdf.gz	445.2 KB	Display	wwPDB validaton report
Full document	5ko5_full_validation.pdf.gz	446.7 KB	Display
Data in XML	5ko5_validation.xml.gz	16.1 KB	Display
Data in CIF	5ko5_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5ko5 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5ko5	HTTPS FTP

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Related structure data

Related structure data	5cxqSC 5cxsC 5ko6C 5tbsC 5tbtC 5tbuC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6b3l-1 6bi9-1 5tbu-1 2a0w-1 6bb7-1 6bi1-1 6b7i-1 6b4t-1 6axa-1 5tbs-1 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: Purine nucleoside phosphorylase

hetero molecules

31.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Purine nucleoside phosphorylase

hetero molecules

A: Purine nucleoside phosphorylase

hetero molecules

A: Purine nucleoside phosphorylase

hetero molecules

defined by author&software
95 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.134, 99.134, 99.134
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	A-621- HOH
2	1	A-673- HOH

#1: Protein	Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase Mass: 31359.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pOPINC / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 References: UniProt: A0A0U3AGT1, UniProt: G4VP83*PLUS, purine-nucleoside phosphorylase
#2: Chemical	ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₅N₃O
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.58 Å³/Da / Density % sol: 52.34 % / Description: cubic shape
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM magnesium chloride, 30mM calcium chloride, 0.1 M MES/imidazole pH 6.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.36→49.567 Å / Num. obs: 69723 / % possible obs: 100 % / Redundancy: 10.6 % / R_merge(I) obs: 0.135 / Net I/σ(I): 15.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.36-1.41	6	1.04	1	100
5.09-70.1	10.7	0.113	1	100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
xia2		data scaling
xia2		data reduction
PHASER		phasing
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CXQ

5cxq

Resolution: 1.36→49.567 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.68

	R_factor	Num. reflection	% reflection
R_free	0.1916	3378	4.86 %
R_work	0.1746	-	-
obs	0.1754	69526	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 93.72 Å² / B_iso mean: 25.4999 Å² / B_iso min: 8.96 Å²

Refinement step

Cycle: final / Resolution: 1.36→49.567 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2162	0	20	347	2529
B_iso mean	-	-	27.56	35.69	-
Num. residues	-	-	-	-	283

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2231
X-RAY DIFFRACTION	f_angle_d	0.872	3025
X-RAY DIFFRACTION	f_chiral_restr	0.082	353
X-RAY DIFFRACTION	f_plane_restr	0.006	393
X-RAY DIFFRACTION	f_dihedral_angle_d	18.175	832

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.36-1.3795	0.375	134	0.3777	2708	2842	98
1.3795-1.4001	0.362	158	0.3465	2670	2828	99
1.4001-1.4219	0.3268	144	0.3205	2717	2861	99
1.4219-1.4453	0.3501	122	0.3188	2792	2914	100
1.4453-1.4702	0.3301	149	0.2915	2679	2828	99
1.4702-1.4969	0.2912	145	0.2658	2709	2854	100
1.4969-1.5257	0.2668	142	0.243	2748	2890	100
1.5257-1.5569	0.207	148	0.2213	2717	2865	100
1.5569-1.5907	0.2267	144	0.2112	2748	2892	100
1.5907-1.6277	0.2343	139	0.1995	2740	2879	100
1.6277-1.6684	0.2109	153	0.1879	2736	2889	100
1.6684-1.7135	0.2098	129	0.183	2744	2873	100
1.7135-1.764	0.1979	153	0.1752	2722	2875	100
1.764-1.8209	0.1827	119	0.1733	2801	2920	100
1.8209-1.886	0.191	141	0.1737	2749	2890	100
1.886-1.9615	0.1794	129	0.17	2751	2880	100
1.9615-2.0508	0.2092	134	0.1581	2789	2923	100
2.0508-2.1589	0.1893	133	0.1569	2772	2905	100
2.1589-2.2942	0.1852	155	0.162	2743	2898	100
2.2942-2.4713	0.1831	95	0.1603	2830	2925	100
2.4713-2.72	0.1667	157	0.161	2765	2922	100
2.72-3.1135	0.1589	171	0.1569	2781	2952	100
3.1135-3.9224	0.1739	143	0.1491	2811	2954	100
3.9224-49.6001	0.1579	141	0.1531	2926	3067	100

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	2.6229	-3.6299	-0.6955	5.4956	0.4069	4.9204	0.0515	-0.0885	0.4844	0.0705	0.101	-0.8651	-0.3204	0.6078	-0.1292	0.1508	-0.0334	0.0021	0.209	-0.0011	0.288	13.0004	101.7951	77.3673
2	3.4331	1.5776	-0.0976	3.6972	-0.6565	1.5387	-0.091	0.0095	-0.1893	-0.2555	0.0748	-0.8296	0.245	0.4845	0.0553	0.2521	0.0641	0.0777	0.3003	-0.031	0.3227	15.5093	84.4295	68.9795
3	1.2584	0.1839	0.1566	1.9685	0.3717	2.1665	0.0007	-0.0391	-0.1382	0.027	0.0454	-0.4393	0.2357	0.3536	-0.015	0.171	0.0492	0.0161	0.2674	0.0224	0.3301	15.2738	88.9494	77.4485
4	0.9852	1.4239	-1.4361	3.1536	-1.9499	3.0288	-0.0064	0.0412	-0.0693	0.0288	-0.0106	-0.2558	0.0057	0.0622	0.0493	0.1253	0.0206	0.0034	0.1582	0.0165	0.1803	4.3812	91.0795	79.7634
5	1.0704	-0.3989	-0.308	1.6682	0.2445	0.7043	0.0535	0.1825	-0.0154	-0.1797	-0.0546	-0.0333	0.0609	-0.005	0.0015	0.1198	0.0239	0.0029	0.1367	0.0108	0.0793	-5.1414	85.8632	71.7393
6	1.6488	0.7677	-2.2433	7.5516	3.1614	6.8013	0.1945	0.6463	0.0214	-0.7711	-0.2604	0.1381	-0.0477	-0.3075	0.002	0.3162	0.0715	-0.0075	0.3611	-0.0126	0.1046	0.5529	78.83	55.5365
7	1.1178	-0.0263	-0.6234	0.7829	0.0294	1.473	-0.0175	0.2381	-0.1989	-0.1373	-0.0619	0.0284	0.1646	-0.1036	0.0819	0.1606	0.0341	0.0072	0.1476	-0.0398	0.1332	-7.1744	72.5033	73.2397
8	1.1281	0.4953	-0.4886	3.5025	-0.1584	0.6619	-0.0483	0.0985	-0.0936	-0.0372	0.016	0.038	0.1071	-0.0158	0.0527	0.1395	0.0312	0.0074	0.1487	-0.008	0.1023	-4.702	76.5908	74.1546
9	2.7611	1.3976	-2.3869	3.7529	-4.4824	8.2769	0.0178	0.128	0.0928	0.0499	0.028	-0.2283	-0.2816	0.0622	0.0317	0.2173	0.0665	0.0387	0.1907	-0.0705	0.1971	8.7279	74.85	65.9148
10	1.9993	2.0011	1.9883	2.0038	1.991	2.0164	0.065	-0.3725	-0.126	-2.3557	0.1847	-1.3172	-0.5537	0.4326	-0.3046	0.2318	0.0448	0.0417	0.1527	-0.0144	0.1372	-2.588	72.149	79.1628

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 23 )	A	5 - 23
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 47 )	A	24 - 47
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 84 )	A	48 - 84
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 108 )	A	85 - 108
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 169 )	A	109 - 169
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 170 through 182 )	A	170 - 182
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 183 through 213 )	A	183 - 213
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 214 through 258 )	A	214 - 258
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 259 through 287 )	A	259 - 287
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 301 through 301 )	A	301

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