PDB-5ifk: Purine nucleoside phosphorylase

ID or keywords:

Entry

Database: PDB / ID: 5ifk

Title

Purine nucleoside phosphorylase

Components

Purine nucleoside phosphorylase

Keywords

TRANSFERASE / Purine nucleoside phosphorylase Hypoxanthine NP-I family Kluyveromyces lactis

Function / homology

Function and homology information

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

Biological species

Kluyveromyces lactis (yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.967 Å

Authors

Thakur, K.G. / Priyanka, A.

Funding support

India, 1items

Citation

Journal: PLoS ONE / Year: 2016
Title: Functional and Structural Characterization of Purine Nucleoside Phosphorylase from Kluyveromyces lactis and Its Potential Applications in Reducing Purine Content in Food
Authors: Mahor, D. / Priyanka, A. / Prasad, G.S. / Thakur, K.G.

History

Deposition	Feb 26, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2017	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ifk.cif.gz	362.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ifk.ent.gz	297.4 KB	Display	PDB format
PDBx/mmJSON format	5ifk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ifk_validation.pdf.gz	460.8 KB	Display	wwPDB validaton report
Full document	5ifk_full_validation.pdf.gz	468.6 KB	Display
Data in XML	5ifk_validation.xml.gz	39.3 KB	Display
Data in CIF	5ifk_validation.cif.gz	57.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/5ifk ftp://data.pdbj.org/pub/pdb/validation_reports/if/5ifk	HTTPS FTP

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Related structure data

Similar structure data	6b71-1 2ai3-1 5tbv-1 1a9t-1 2ai2-1 3e0q-d 5ugf-1 5tbt-1 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
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Purine nucleoside phosphorylase

B: Purine nucleoside phosphorylase

C: Purine nucleoside phosphorylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.780, 80.780, 231.161
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase Mass: 34236.938 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_C16621g / Plasmid: pET28a-BSaI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6CSZ6, purine-nucleoside phosphorylase
#2: Chemical	ChemComp-HPA / HYPOXANTHINE Mass: 136.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₄N₄O
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.12 Å³/Da / Density % sol: 41.97 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M sodium acetate trihydrate, 8% PEG 4000, pH 4.6

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Data collection

Diffraction source

Source:

ROTATING ANODE / Type: OTHER / Wavelength: 0.9762 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE

Radiation

Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 1.967→231.161 Å / Num. obs: 60087 / % possible obs: 99.7 % / Redundancy: 4.8 % / B_iso Wilson estimate: 26.38 Å² / R_sym value: 0.059 / Net I/av σ(I): 8.744 / Net I/σ(I): 16

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.97-2.07	4.6	0.34	2.2	1	98.6
2.07-2.2	4.8	0.22	3.5	1	99.7
2.2-2.35	4.8	0.147	5.2	1	99.8
2.35-2.54	4.8	0.105	7.2	1	99.8
2.54-2.78	4.9	0.077	9.5	1	100
2.78-3.11	4.9	0.053	13.5	1	100
3.11-3.59	4.9	0.043	15.1	1	100
3.59-4.4	4.9	0.048	12.1	1	100
4.4-6.22	4.8	0.04	14	1	100
6.22-39.787	4.7	0.023	25.7	1	98.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	39.79 Å
Translation	2.5 Å	39.79 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data collection
SCALA	3.3.20	data scaling
PHASER	2.3.0	phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.967→39.787 Å / SU ML: 0.19 / σ(F): 1.45 / Phase error: 19.52

	R_factor	Num. reflection	% reflection
R_free	0.1987	3023	5.04 %
R_work	0.1559	-	-
obs	0.158	60033	99.63 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 106.13 Å² / B_iso mean: 35.0795 Å² / B_iso min: 11.04 Å²

Refinement step

Cycle: final / Resolution: 1.967→39.787 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6782	0	30	626	7438
B_iso mean	-	-	26.58	39.48	-
Num. residues	-	-	-	-	880

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6965
X-RAY DIFFRACTION	f_angle_d	1.076	9436
X-RAY DIFFRACTION	f_chiral_restr	0.044	1061
X-RAY DIFFRACTION	f_plane_restr	0.005	1221
X-RAY DIFFRACTION	f_dihedral_angle_d	12.014	2527

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.967-1.9978	0.2979	127	0.2207	2456	2583	96
1.9978-2.0305	0.2109	129	0.1996	2607	2736	99
2.0305-2.0655	0.2624	115	0.1944	2599	2714	100
2.0655-2.1031	0.2605	146	0.1846	2544	2690	100
2.1031-2.1435	0.2201	147	0.1753	2601	2748	100
2.1435-2.1873	0.2151	123	0.1621	2648	2771	100
2.1873-2.2348	0.2398	149	0.1606	2552	2701	100
2.2348-2.2868	0.1924	137	0.1523	2592	2729	100
2.2868-2.344	0.1856	158	0.1545	2544	2702	100
2.344-2.4074	0.2069	135	0.156	2637	2772	100
2.4074-2.4782	0.2019	160	0.1596	2569	2729	100
2.4782-2.5582	0.2253	125	0.167	2603	2728	100
2.5582-2.6496	0.243	126	0.1723	2602	2728	100
2.6496-2.7556	0.2275	126	0.1729	2611	2737	100
2.7556-2.881	0.2064	157	0.1723	2610	2767	100
2.881-3.0329	0.2456	149	0.1674	2585	2734	100
3.0329-3.2228	0.2054	137	0.1662	2595	2732	100
3.2228-3.4715	0.204	132	0.1504	2597	2729	100
3.4715-3.8206	0.194	133	0.1457	2634	2767	100
3.8206-4.3729	0.1499	146	0.1232	2600	2746	100
4.3729-5.507	0.1677	129	0.1284	2613	2742	100
5.507-39.7953	0.1602	137	0.1567	2611	2748	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	7.982	-5.1869	1.2278	3.8032	-0.8336	6.1582	-0.3323	0.0588	0.9434	0.3546	0.2528	-1.533	-0.4205	0.6871	0.0323	0.2109	-0.0243	-0.0518	0.414	0.0636	0.4033	50.4203	-42.8337	-21.8322
2	6.9736	-0.8137	1.3532	6.8125	-0.2647	3.3017	-0.0557	-0.2465	-0.4869	0.4212	-0.0495	0.1055	0.5277	0.2219	0.0872	0.2965	0.0981	0.0299	0.209	0.0333	0.2854	41.7328	-56.0724	-22.0948
3	2.0759	-0.4346	-0.6223	1.3092	0.3193	1.123	-0.0156	-0.0508	-0.2842	0.1746	-0.0538	0.1036	0.2323	-0.0314	0.0484	0.243	-0.0204	-0.0008	0.122	0.0102	0.1947	23.1658	-44.6553	-24.6992
4	4.4243	-3.3992	-3.6346	7.7532	5.1123	6.6105	-0.591	-0.1656	-0.7972	0.5589	0.0005	0.4499	1.2267	-0.18	0.5702	0.4321	-0.0068	-0.055	0.2018	0.0305	0.4958	24.4841	-59.5773	-22.8285
5	5.6676	3.6516	-4.4023	6.755	-5.4487	7.0474	-0.0196	0.013	-0.0878	0.254	0.0882	-0.6729	-0.4827	0.8865	0.1474	0.2532	-0.1514	0.0439	0.4009	-0.1596	0.3214	38.2003	-1.0573	-16.7404
6	4.3078	0.8373	0.4599	2.4587	-0.8913	2.2415	-0.0101	0.4703	0.1912	-0.3075	0.2075	-0.1311	-0.3411	0.9576	-0.1511	0.3322	-0.1285	0.1148	0.4579	-0.0836	0.3038	35.9983	0.0659	-32.7699
7	0.5427	-0.605	0.5408	7.1373	-5.2905	4.2178	-0.0175	0.0687	0.135	-0.3173	0.1839	-0.4457	-0.0327	0.2986	-0.0268	0.2495	-0.0999	0.074	0.233	-0.0647	0.2823	32.833	-10.6637	-29.7347
8	2.208	-0.3777	0.1909	2.4325	0.3326	3.5984	-0.0536	-0.1787	0.0304	0.5153	0.2949	-0.4521	-0.049	0.3307	-0.1767	0.1594	-0.0381	0.036	0.2008	-0.0866	0.1884	31.0683	-7.1197	-20.0881
9	1.1242	0.3257	0.0916	1.3924	0.9171	3.0485	0.0404	-0.0362	0.1195	0.0061	-0.0143	0.0766	-0.0143	0.0313	-0.028	0.0921	-0.0081	0.021	0.0906	-0.0016	0.1111	19.3345	-13.887	-25.9212
10	2.299	-0.5418	0.3293	3.5113	-1.7031	5.1185	0.0336	0.3136	0.2144	-0.3099	0.0705	0.1758	-0.3195	-0.1753	-0.1237	0.1533	-0.0267	-0.0099	0.133	0.0321	0.1454	15.4219	-8.5089	-41.305
11	1.0194	-0.8279	-0.4404	1.0637	0.8223	1.4919	0.0852	-0.0185	-0.0346	0.027	-0.0433	0.0208	0.0797	-0.0292	-0.043	0.1503	-0.0218	0.0178	0.122	0.0266	0.1088	20.6987	-21.977	-29.2297
12	1.872	1.5914	0.4916	4.8684	-0.4066	1.0351	-0.04	0.2999	-0.5566	-0.986	0.2112	-0.4737	0.2643	-0.0288	-0.14	0.3241	-0.0452	-0.0076	0.2517	-0.0421	0.2484	20.9732	-32.44	-41.6738
13	2.3546	-2.169	-0.6091	9.0297	-0.5387	4.2353	0.1206	0.273	0.0981	-0.7216	-0.0275	-0.2207	-0.0597	0.1975	-0.0261	0.1752	-0.088	0.0242	0.2423	0.0375	0.2036	26.9068	-10.3732	-43.9031
14	6.8355	-3.4378	-5.0713	4.2066	4.6231	7.0114	-0.0422	-1.0012	-0.1831	0.8186	0.4308	-0.4718	0.3416	1.3381	-0.3977	0.9892	-0.0233	-0.2849	0.468	0.0132	0.4501	24.9723	-30.9777	14.1507
15	3.9069	-0.2501	0.7155	0.1314	-0.5142	3.922	-0.0811	-0.4748	0.3147	0.8473	-0.0583	0.073	0.0154	-0.1695	0.0757	0.9038	-0.1225	0.0906	0.3443	-0.045	0.293	10.7444	-23.4154	14.3243
16	6.0927	3.8035	-6.831	3.5367	-4.7455	9.5564	0.3222	-0.2081	-0.217	0.7673	-0.235	0.1157	-0.3577	-0.0972	-0.1611	0.6005	-0.0688	0.018	0.2579	-0.0284	0.2536	14.3675	-22.632	3.1101
17	3.2545	-1.7477	1.8212	3.867	-4.3199	5.4868	0.0974	-0.3283	-0.0772	0.6612	-0.1535	-0.1067	0.2025	0.2239	0.0539	0.5745	-0.0731	-0.0164	0.1578	-0.0144	0.1812	14.7013	-30.0529	3.2414
18	6.6311	-3.1401	0.7368	3.3303	-0.3904	1.235	0.0062	-0.2002	-0.0837	0.3471	-0.0416	0.0029	0.2364	0.0121	0.0235	0.3161	-0.0727	0.0564	0.1389	-0.0037	0.1649	12.1498	-33.5585	-8.6268
19	1.0534	0.6535	-1.3636	0.4249	-0.7541	2.1542	-0.036	0.085	-0.0477	0.4088	-0.0402	0.5641	0.2402	-0.5449	0.0209	0.3672	-0.13	0.2489	0.3096	-0.0561	0.4274	-4.6385	-28.9037	-3.0325
20	1.3802	0.2892	0.3241	1.9487	-0.3238	2.4985	0.0918	-0.0188	-0.0775	0.2167	-0.0745	0.0736	0.2561	-0.0163	-0.0194	0.1822	-0.0439	0.0534	0.1385	-0.0277	0.1407	11.1099	-26.2543	-12.8247
21	1.5283	1.6991	-2.5249	2.2578	-1.99	5.1412	0.0769	0.1994	0.3271	0.1847	0.1988	0.4037	-0.4508	-0.7288	-0.3368	0.1922	0.0087	0.0496	0.2281	-0.0051	0.3187	3.6252	-14.1551	-20.9007
22	3.395	1.3164	-2.8959	0.9398	-2.3854	6.4881	-0.0688	-0.095	0.3091	0.6884	0.0068	0.5473	0.0536	-0.5471	-0.4091	0.527	-0.0847	0.2542	0.3071	-0.1303	0.3172	-0.2015	-18.5085	1.3883

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 27 )	A	5 - 27
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 85 )	A	28 - 85
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 280 )	A	86 - 280
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 281 through 306 )	A	281 - 306
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 27 )	B	5 - 27
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 28 through 85 )	B	28 - 85
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 86 through 104 )	B	86 - 104
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 105 through 118 )	B	105 - 118
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 119 through 180 )	B	119 - 180
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 181 through 207 )	B	181 - 207
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 208 through 246 )	B	208 - 246
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 247 through 280 )	B	247 - 280
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 281 through 306 )	B	281 - 306
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 27 )	C	6 - 27
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 28 through 85 )	C	28 - 85
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 86 through 104 )	C	86 - 104
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 105 through 132 )	C	105 - 132
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 133 through 180 )	C	133 - 180
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 181 through 207 )	C	181 - 207
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 208 through 246 )	C	208 - 246
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 247 through 280 )	C	247 - 280
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 281 through 306 )	C	281 - 306

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