PDB-9mg9: Crystal structure of Purine nucleoside phosphorylase from Trichom...

ID or keywords:

Entry

Database: PDB / ID: 9mg9

Title

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (glycerol bound)

Components

Purine nucleoside phosphorylase, putative

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Purine nucleoside phosphorylase / Trichomonas vaginalis

Function / homology

Function and homology information

uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (glycerol bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mg9.cif.gz	807.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9mg9.ent.gz	684 KB	Display	PDB format
PDBx/mmJSON format	9mg9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/9mg9 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/9mg9	HTTPS FTP

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Related structure data

Similar structure data	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, putative

B: Purine nucleoside phosphorylase, putative

C: Purine nucleoside phosphorylase, putative

D: Purine nucleoside phosphorylase, putative

E: Purine nucleoside phosphorylase, putative

F: Purine nucleoside phosphorylase, putative

hetero molecules

161 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	102.806, 50.947, 153.150
Angle α, β, γ (deg.)	90.00, 95.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Purine nucleoside phosphorylase, putative Mass: 26643.428 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_454490 / Plasmid: TrvaA.01033.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2EU62
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1171 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.74 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: JCSG+ A5: 0.2 M magnesium formate, pH 5.9, 20% (w/v) PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. glycerol acquired from the cryo. plate 14430 well A5 drop 2, Puck: PSL1005, Cryo: 80% ...Details: JCSG+ A5: 0.2 M magnesium formate, pH 5.9, 20% (w/v) PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. glycerol acquired from the cryo. plate 14430 well A5 drop 2, Puck: PSL1005, Cryo: 80% crystallant + 20% glycerol.

Crystal

Density Matthews: 2.5 Å³/Da / Density % sol: 50.74 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: JCSG+ A5: 0.2 M magnesium formate, pH 5.9, 20% (w/v) PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. glycerol acquired from the cryo. plate 14430 well A5 drop 2, Puck: PSL1005, Cryo: 80% ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.64→152.41 Å / Num. obs: 181573 / % possible obs: 93.6 % / Redundancy: 6.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.036 / R_rim(I) all: 0.092 / Χ²: 1.11 / Net I/σ(I): 13.3 / Num. measured all: 1188075
Reflection shell	Resolution: 1.64→1.68 Å / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 1.183 / Num. measured all: 96470 / Num. unique obs: 14198 / CC_1/2: 0.648 / R_pim(I) all: 0.486 / R_rim(I) all: 1.281 / Χ²: 0.87 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	dev_5438	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.64→44.54 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1786	9076	5 %
R_work	0.1522	-	-
obs	0.1535	181517	93.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.64→44.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10788	0	78	1171	12037

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11327
X-RAY DIFFRACTION	f_angle_d	1.005	15413
X-RAY DIFFRACTION	f_dihedral_angle_d	12.65	4184
X-RAY DIFFRACTION	f_chiral_restr	0.06	1788
X-RAY DIFFRACTION	f_plane_restr	0.009	1992

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 (%)
1.64-1.66	0.2776	330	0.2503	6012	X-RAY DIFFRACTION	100
1.66-1.68	0.253	317	0.2387	6089	X-RAY DIFFRACTION	100
1.68-1.7	0.2699	318	0.227	6155	X-RAY DIFFRACTION	100
1.7-1.72	0.2436	261	0.2291	4980	X-RAY DIFFRACTION	98
1.72-1.74	0.2811	299	0.223	5754	X-RAY DIFFRACTION	98
1.74-1.77	0.2502	345	0.2086	6047	X-RAY DIFFRACTION	100
1.77-1.79	0.2288	321	0.1991	6078	X-RAY DIFFRACTION	100
1.79-1.82	0.2316	332	0.1961	6185	X-RAY DIFFRACTION	100
1.82-1.85	0.243	320	0.2011	6054	X-RAY DIFFRACTION	100
1.85-1.88	0.2263	272	0.1984	6091	X-RAY DIFFRACTION	99
1.88-1.91	0.2124	245	0.1864	4691	X-RAY DIFFRACTION	77
1.91-1.94	0.2159	235	0.1838	4346	X-RAY DIFFRACTION	74
1.95-1.98	0.2035	269	0.1669	5223	X-RAY DIFFRACTION	99
1.98-2.02	0.1982	327	0.1622	6131	X-RAY DIFFRACTION	100
2.02-2.06	0.1926	298	0.1492	5336	X-RAY DIFFRACTION	98
2.08-2.11	0.1947	253	0.1575	4905	X-RAY DIFFRACTION	99
2.11-2.17	0.1856	311	0.1521	6120	X-RAY DIFFRACTION	100
2.17-2.23	0.191	293	0.1513	6165	X-RAY DIFFRACTION	100
2.23-2.29	0.1759	255	0.1499	5175	X-RAY DIFFRACTION	84
2.29-2.37	0.1712	330	0.1443	6076	X-RAY DIFFRACTION	100
2.37-2.45	0.1564	281	0.1452	6247	X-RAY DIFFRACTION	100
2.45-2.55	0.1728	337	0.1434	6141	X-RAY DIFFRACTION	100
2.55-2.66	0.1695	299	0.1364	5711	X-RAY DIFFRACTION	99
2.68-2.8	0.1757	294	0.1452	5260	X-RAY DIFFRACTION	99
2.8-2.98	0.1774	340	0.1542	6142	X-RAY DIFFRACTION	100
2.98-3.21	0.1813	318	0.15	6163	X-RAY DIFFRACTION	99
3.21-3.53	0.1626	307	0.1412	5382	X-RAY DIFFRACTION	88
3.53-4.04	0.1583	272	0.1366	5099	X-RAY DIFFRACTION	82
4.04-5.09	0.1285	336	0.1093	6302	X-RAY DIFFRACTION	100
5.09-44.54	0.1779	361	0.1596	6381	X-RAY DIFFRACTION	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	0.0283	-0.0123	0.0266	0.0129	0.0036	0.037	-0.0019	-0.3279	-0.1131	0.1186	0.0171	-0.0614	0.0628	-0.0938	0	0.1978	-0.0046	0.0065	0.2596	0.0427	0.2115	7.255	-7.5965	76.9876
2	0.4054	-0.0973	0.0993	0.1527	0.1067	0.3755	0.0317	-0.0548	-0.0141	-0.0212	-0.0607	-0.0032	-0.0419	-0.0323	-0	0.1533	-0.0039	0.013	0.1412	0.0047	0.1779	4.6637	1.8805	61.6138
3	0.01	-0.0006	0.0058	0.0174	-0.0278	0.0396	-0.0017	-0.0778	0.0379	0.1029	0.0738	0.0671	-0.0237	-0.1398	-0	0.2103	-0.0081	0.0267	0.2154	-0.0052	0.2106	-2.2211	6.7214	73.5209
4	0.0171	-0.0038	0.007	0.004	-0.011	0.0278	-0.0068	0.0384	0.0502	-0.1844	-0.0371	0.0811	-0.1908	-0.2657	-0	0.2984	0.0678	-0.0874	0.2818	-0.0318	0.2647	-19.1632	7.6676	31.4892
5	0.1283	0.083	0.0048	0.0949	-0.0176	0.2678	0.0268	-0.0334	-0.0264	-0.1219	-0.0691	0.0078	-0.0211	-0.0513	-0.0116	0.1855	0.04	-0.038	0.1397	-0.0241	0.1598	-8.1418	2.354	39.2046
6	0.0041	0.0034	-0.0041	0.0047	-0.0042	0.007	0.0016	-0.0849	0.0025	0.0543	0.0267	0.0223	-0.0438	-0.0576	0	0.1802	-0.0052	-0.0154	0.2816	-0.0201	0.2269	-16.4263	-0.7623	53.3632
7	0.1231	-0.0397	0.0819	0.0082	-0.0237	0.1506	0.0554	0.0123	-0.0558	-0.1638	-0.0649	0.0766	0.0778	-0.0831	-0	0.2465	0.012	-0.0311	0.1649	-0.0171	0.204	-4.2571	-8.0746	41.7876
8	0.0222	-0.0165	0.0242	0.0143	-0.0214	0.0274	0.083	-0.0163	-0.0915	-0.0484	0.1261	0.0912	0.0848	-0.1284	-0	0.2766	0.0159	-0.0855	0.3368	-0.0475	0.3536	-20.9817	-6.9375	41.3079
9	0.0289	0.0188	0.0038	0.0144	0.0112	0.0266	0.0066	-0.2072	0.1046	0.151	-0.0242	-0.1278	-0.0956	-0.0164	0	0.1843	-0.0186	-0.0465	0.1885	0.0001	0.2634	29.2482	4.4235	77.4332
10	0.3304	-0.1213	0.2295	0.1518	-0.1209	0.27	0.0552	0.0803	0.015	0.0064	-0.0724	-0.1041	0.0485	0.0526	-0.0023	0.1486	0.0019	-0.0161	0.1606	0.0203	0.2519	31.8681	-3.9405	61.4136
11	0.0252	-0.0119	0.0184	0.0125	0.0069	0.0376	0.0142	-0.0692	-0.0035	0.0595	0.0074	-0.0167	0.0303	0.0051	-0	0.2018	-0.0251	-0.0574	0.1839	0.0387	0.3377	38.834	-9.748	72.9246
12	0.031	0.0053	-0.0076	0.015	0.0161	0.0238	-0.0507	0.0385	-0.0507	-0.1138	-0.0035	0.0674	0.1061	-0.1827	0	0.4138	0.0196	-0.0635	0.1996	-0.0183	0.2009	-8.6491	-4.5913	12.1484
13	0.2119	0.0379	0.0435	0.1798	-0.1487	0.5501	-0.006	0.0116	-0.0025	-0.1651	-0.0625	0.0254	0.0076	0.0718	-0.1385	0.3313	0.0361	-0.0178	0.1522	-0.0015	0.1507	6.6423	3.6416	17.8458
14	0.0304	0.017	0.0125	0.0111	-0.0024	0.0279	-0.0213	-0.0058	0.0027	-0.0566	-0.046	0.0492	-0.0091	-0.0444	0	0.4755	0.0429	-0.042	0.1674	-0.0154	0.1844	0.3202	9.5428	6.019
15	0.0424	0.0003	0.0247	-0.0005	0.0033	0.0218	-0.0133	0.029	-0.0993	-0.0233	-0.0523	-0.0597	0.0955	0.1517	-0.0519	0.2887	0.2139	0.1479	0.7547	-0.0059	0.4081	51.1921	-11.6582	30.6411
16	0.014	0.003	-0.0093	0.0012	-0.0026	0.0073	0.0262	0.0073	-0.0283	-0.0034	-0.0023	-0.0595	-0.0363	0.0483	0.0101	0.2292	0.0449	0.2177	0.8464	0.0661	0.4793	60.4404	-2.5296	30.9608
17	0.0048	0.0004	-0.0047	0.0006	0.0023	-0.0005	-0.0294	0.1297	-0.0199	-0.0807	-0.0054	-0.2722	0.0754	0.2278	-0.0793	0.1572	0.1831	0.1193	0.7234	0.0848	0.3507	50.4786	-6.9666	32.9499
18	0.023	-0.0208	0.0309	0.0502	-0.0721	0.1147	0.0344	0.1868	0.0693	0.0078	-0.1368	-0.0018	-0.0049	0.4368	-0.0189	0.2457	0.0069	0.0698	0.5858	0.1046	0.4036	47.3574	3.9344	42.3935
19	0.0875	0.0343	-0.0697	0.016	-0.027	0.0554	0.0347	0.0783	0.0475	-0.1182	-0.1521	-0.098	0.0733	0.2415	-0.0229	0.1638	0.0375	0.0349	0.3167	0.0468	0.2614	34.0598	-2.593	44.2001
20	0.0065	-0.0105	0.0015	0.0181	-0.0027	0.0011	-0.0189	-0.0248	-0.0241	0.02	0.0093	-0.0182	0.0237	-0.0026	0.0062	0.1245	0.0149	0.0109	0.4919	0.0843	0.39	53.026	-0.791	53.3621
21	0.097	-0.0711	0.0366	0.1005	0.0691	0.2692	0.0276	0.2211	0.1007	-0.0902	-0.0738	-0.1526	-0.1187	0.417	-0.0127	0.1704	-0.0026	0.0326	0.3855	0.0911	0.3119	38.8687	5.555	42.7905
22	0.0073	0.0114	0.0199	0.0166	0.0288	0.05	-0.0023	0.1287	0.1473	-0.0296	0.0109	0.0229	-0.095	0.1993	-0.0014	0.229	-0.0413	0.0708	0.524	0.1453	0.4804	46.2026	12.7517	41.2805
23	0.0058	0.0039	-0.0084	0.0242	0.0115	0.0263	-0.0044	0.078	0.0422	-0.0343	0.0672	-0.0377	-0.0565	0.0588	0.0066	0.1748	0.0048	0.1342	0.7402	0.1654	0.5711	57.5952	6.2655	41.8952
24	0.0168	-0.0137	0.0223	0.0136	-0.0226	0.0347	-0.0253	0.1868	0.0312	-0.1304	-0.0861	-0.1404	-0.0041	0.2153	-0.2257	0.3173	0.0268	0.2302	0.8767	0.1618	0.3367	45.142	6.6585	12.6222
25	0.2337	-0.0804	0.0188	0.3387	0.08	0.0374	0.0073	0.3557	0.0373	-0.2588	-0.1554	-0.0632	0.0651	0.4359	-0.2934	0.305	0.0797	0.1024	0.5963	0.0933	0.2017	32.5478	2.1624	18.0119
26	0.0115	-0	0.0045	-0.0003	0.0004	0.002	0.0549	0.0398	0.0334	-0.0388	-0.0057	0.0111	-0.0051	-0.0193	-0.0061	0.4343	0.1156	0.0777	0.5895	-0.0179	0.1354	24.2254	0.4027	3.6639
27	0.1323	-0.0042	0.0516	0.0193	-0.0081	0.0493	0.0569	0.2843	-0.0771	-0.1071	-0.0621	-0.0428	0.1697	0.3681	0.0015	0.3536	0.1249	0.0501	0.4078	0.0107	0.2196	26.2272	-6.039	21.1093
28	0.0409	0.0253	0.0219	0.0277	0.0094	0.0197	-0.0305	0.2598	-0.0825	-0.0386	0.0243	-0.1005	0.0967	0.2104	0.0031	0.4899	0.222	0.1411	0.6592	-0.0121	0.2896	34.1128	-9.6364	9.7324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 214 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 215 through 236 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 0 through 41 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 42 through 131 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 132 through 144 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 145 through 214 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 215 through 236 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 0 through 41 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 42 through 214 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 215 through 236 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 0 through 41 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 42 through 214 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 215 through 236 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 0 through 22 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 23 through 41 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 42 through 79 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 80 through 103 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 104 through 131 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 132 through 144 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 145 through 195 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 196 through 214 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 215 through 236 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 0 through 41 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 42 through 131 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 132 through 144 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 145 through 195 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 196 through 236 )

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