PDB-8swp: Structure of K. lactis PNP bound to hypoxanthine

ID or keywords:

Entry

Database: PDB / ID: 8swp

Title

Structure of K. lactis PNP bound to hypoxanthine

Components

Purine nucleoside phosphorylase

Keywords

TRANSFERASE / PENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE

Function / homology

Function and homology information

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

Biological species

Kluyveromyces lactis NRRL Y-1140 (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Fedorov, E. / Ghosh, A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM041916	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA013330	United States

Citation

Journal: Biochemistry / Year: 2023
Title: Phosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity.
Authors: Minnow, Y.V.T. / Schramm, V.L. / Almo, S.C. / Ghosh, A.

History

Deposition	May 19, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 22, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8swp.cif.gz	658.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8swp.ent.gz	549.3 KB	Display	PDB format
PDBx/mmJSON format	8swp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8swp_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8swp_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8swp_validation.xml.gz	61.2 KB	Display
Data in CIF	8swp_validation.cif.gz	84.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sw/8swp ftp://data.pdbj.org/pub/pdb/validation_reports/sw/8swp	HTTPS FTP

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Related structure data

Related structure data	8swqC 8swrC 8swsC 8swtC 8swuC C: citing same article (ref.)
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
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

D: Purine nucleoside phosphorylase

E: Purine nucleoside phosphorylase

F: Purine nucleoside phosphorylase

hetero molecules

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

1

A: Purine nucleoside phosphorylase

B: Purine nucleoside phosphorylase

C: Purine nucleoside phosphorylase

hetero molecules

defined by author&software
Evidence: gel filtration, Superdex S200
102 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Purine nucleoside phosphorylase

E: Purine nucleoside phosphorylase

F: Purine nucleoside phosphorylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.211, 110.825, 97.718
Angle α, β, γ (deg.)	90.00, 108.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Purine nucleoside phosphorylase Mass: 33729.617 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast) Gene: KLLA0_C16621g / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRIL / References: UniProt: Q6CSZ6
#2: Chemical	ChemComp-HPA / HYPOXANTHINE Mass: 136.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₄N₄O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.18 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% (w/v) PEG 3,350, 0.185 M Ammonium acetate and 0.1 M BIS-TRIS

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 205816 / % possible obs: 98.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.082 / Χ²: 1.228 / Net I/σ(I): 9.2 / Num. measured all: 757592

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.1-2.14	3.5	0.913	10389	0.983	1	99.1
2.14-2.18	3.5	0.804	10289	1.027	1	99.4
2.18-2.22	3.5	0.678	10294	1.037	1	99.3
2.22-2.26	3.5	0.586	10346	1.45	1	99
2.26-2.31	3.6	0.617	10191	1.114	1	99.1
2.31-2.37	3.6	0.466	10358	1.056	1	99
2.37-2.42	3.6	0.4	10287	1.074	1	99.2
2.42-2.49	3.6	0.335	10305	1.075	1	99
2.49-2.56	3.7	0.29	10313	1.116	1	99
2.56-2.65	3.7	0.232	10350	1.103	1	99.1
2.65-2.74	3.7	0.201	10252	1.252	1	98.9
2.74-2.85	3.7	0.148	10344	1.102	1	99.2
2.85-2.98	3.8	0.116	10260	1.122	1	99.3
2.98-3.14	3.8	0.099	10400	1.296	1	99.7
3.14-3.33	3.8	0.086	10383	1.433	1	99.9
3.33-3.59	3.7	0.073	10375	1.605	1	100
3.59-3.95	3.7	0.063	10402	1.42	1	100
3.95-4.52	3.9	0.046	10362	1.709	1	100
4.52-5.7	3.9	0.036	10405	1.289	1	99.5
5.7-50	3.7	0.029	9511	1.195	1	91.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data reduction
SHELXDE		phasing
DM		phasing
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.1→39.61 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2359	5227	5 %
R_work	0.1994	-	-
obs	0.2013	104506	98.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→39.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12911	0	56	440	13407

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.546
X-RAY DIFFRACTION	f_dihedral_angle_d	4.67	1840
X-RAY DIFFRACTION	f_chiral_restr	0.041	2045
X-RAY DIFFRACTION	f_plane_restr	0.004	2325

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 (%)
2.1-2.12	0.3587	174	0.2993	3149	X-RAY DIFFRACTION	93
2.12-2.15	0.3118	159	0.2772	3269	X-RAY DIFFRACTION	99
2.15-2.17	0.2995	182	0.2772	3341	X-RAY DIFFRACTION	99
2.17-2.2	0.3761	153	0.2604	3317	X-RAY DIFFRACTION	100
2.2-2.23	0.3078	165	0.2714	3321	X-RAY DIFFRACTION	99
2.23-2.26	0.3573	179	0.3217	3274	X-RAY DIFFRACTION	99
2.26-2.29	0.316	180	0.2761	3305	X-RAY DIFFRACTION	99
2.29-2.33	0.3206	160	0.2566	3299	X-RAY DIFFRACTION	99
2.33-2.36	0.2762	183	0.2482	3285	X-RAY DIFFRACTION	99
2.36-2.4	0.2686	166	0.2358	3322	X-RAY DIFFRACTION	99
2.4-2.44	0.2885	173	0.2315	3318	X-RAY DIFFRACTION	99
2.44-2.49	0.2824	159	0.2299	3288	X-RAY DIFFRACTION	99
2.49-2.54	0.2585	168	0.2274	3309	X-RAY DIFFRACTION	99
2.54-2.59	0.255	179	0.2309	3300	X-RAY DIFFRACTION	99
2.59-2.64	0.2699	187	0.2236	3304	X-RAY DIFFRACTION	99
2.64-2.7	0.2704	177	0.2241	3297	X-RAY DIFFRACTION	99
2.7-2.77	0.2775	182	0.2251	3291	X-RAY DIFFRACTION	99
2.77-2.85	0.2887	194	0.2279	3300	X-RAY DIFFRACTION	99
2.85-2.93	0.2825	195	0.2272	3261	X-RAY DIFFRACTION	99
2.93-3.03	0.2666	164	0.2225	3358	X-RAY DIFFRACTION	99
3.03-3.13	0.2544	160	0.217	3351	X-RAY DIFFRACTION	100
3.13-3.26	0.2448	176	0.2123	3340	X-RAY DIFFRACTION	100
3.26-3.41	0.2546	176	0.1992	3332	X-RAY DIFFRACTION	100
3.41-3.59	0.2443	166	0.1975	3357	X-RAY DIFFRACTION	100
3.59-3.81	0.2183	170	0.183	3375	X-RAY DIFFRACTION	100
3.81-4.11	0.1834	173	0.1646	3369	X-RAY DIFFRACTION	100
4.11-4.52	0.1858	186	0.1485	3315	X-RAY DIFFRACTION	100
4.52-5.17	0.1852	187	0.1512	3386	X-RAY DIFFRACTION	100
5.17-6.51	0.2193	191	0.1752	3378	X-RAY DIFFRACTION	100
6.51-39.61	0.1686	163	0.1691	3168	X-RAY DIFFRACTION	92

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	3.4959	-0.1584	-1.0286	3.4707	-0.4533	3.8027	-0.0313	-0.3216	-0.554	0.5672	-0.1905	0.2877	0.7528	-0.372	0.203	0.6948	-0.2269	0.0694	0.604	0.0137	0.4561	72.1604	-5.3696	58.2988
2	1.8014	-0.3613	-0.5452	1.0719	0.2273	2.4493	-0.0489	-0.0359	0.0342	0.0038	-0.0421	0.1763	-0.0964	-0.727	0.065	0.2463	-0.013	-0.002	0.5485	-0.0761	0.2957	74.2483	15.6267	50.7917
3	6.1767	0.5689	-1.594	3.3173	-1.6837	4.0003	-0.0536	-0.0241	-0.8977	-0.0647	-0.0174	-0.4511	0.1897	0.2041	0.1064	0.3598	-0.0213	-0.0402	0.3877	-0.1112	0.6412	118.1484	7.6921	44.073
4	3.6793	-0.064	0.5596	1.2195	0.188	1.382	-0.0493	0.0925	0.2365	-0.0789	0.0719	-0.1113	-0.2929	0.0602	-0.0044	0.3222	-0.043	0.0185	0.2798	-0.0823	0.2945	103.6377	20.924	36.9762
5	4.4903	-0.0988	-0.314	1.1617	0.0933	2.7482	0.0422	0.4222	-0.0897	-0.0882	0.0698	-0.0624	-0.0018	-0.183	-0.1059	0.3612	-0.023	-0.0073	0.3161	-0.0891	0.2373	93.4072	12.42	29.2083
6	3.3237	0.6339	0.5948	7.7184	-1.868	2.4234	-0.0005	-0.5375	0.2567	0.4887	-0.0154	-0.3113	-0.4311	-0.046	-0.0147	0.4728	-0.0409	-0.0561	0.6615	-0.2308	0.473	96.1143	35.8524	83.325
7	2.2606	1.0289	-1.3048	2.6368	-2.5471	7.3934	-0.0394	-0.4729	0.3872	-0.4833	0.0246	-0.2535	-0.2564	0.1981	0.0819	0.4889	-0.0473	0.0744	0.3955	-0.2257	0.4607	91.9852	35.7497	68.2589
8	1.5963	0.6547	0.1079	2.9562	1.1266	2.0226	0.0801	-0.2863	0.2954	-0.1408	0.0568	-0.0152	-0.5684	-0.1354	-0.1189	0.4285	0.0455	0.0145	0.5034	-0.1623	0.4126	84.2474	34.5806	64.8972
9	0.3443	-0.0097	0.7369	0.3391	0.2365	1.8152	0.1163	-0.1765	0.412	-0.2994	0.1115	-0.279	-0.7613	0.3699	-0.1677	0.5841	-0.0901	0.1147	0.349	-0.1948	0.6207	94.6185	39.8826	57.9216
10	4.3463	0.2322	0.6908	3.5134	1.2284	3.7282	-0.0229	0.2223	-0.9729	-0.2134	0.035	-0.0597	0.8833	-0.1125	-0.0416	0.6878	0.0101	-0.0271	0.4359	-0.0622	0.5629	56.0602	-10.4325	80.5706
11	1.9666	-0.0868	0.36	1.6183	-0.2094	1.3189	-0.0024	0.0116	-0.1533	-0.0293	-0.0382	-0.13	0.198	0.1994	0.0465	0.2752	0.0024	-0.0193	0.4046	0.0202	0.2947	58.0572	10.6543	87.3442
12	7.0955	0.0604	-0.5274	3.2387	1.1328	3.7176	0.017	-0.2699	-0.689	0.1222	-0.1195	0.2632	0.3516	-0.2322	0.0981	0.3834	-0.149	-0.0435	0.5068	0.0442	0.4756	13.672	9.8826	94.002
13	3.6671	-0.2902	0.251	1.059	0.2395	1.0026	-0.0356	-0.6886	-0.0408	0.2144	0.0593	0.0835	0.0927	-0.0764	-0.0141	0.3201	-0.067	0.0048	0.5623	0.0284	0.2365	32.8454	19.1714	103.2984
14	6.5133	-3.4745	2.0476	9.3679	-2.0632	5.4837	0.0468	0.6827	-0.2597	-1.4629	-0.1107	0.4774	0.0174	-0.078	0.0247	0.4479	-0.0305	-0.0769	0.5988	-0.114	0.4015	40.5974	23.9397	48.6384
15	4.8129	-0.2588	2.0553	9.1644	1.9862	3.3972	-0.0716	0.2539	0.2806	-0.3586	-0.0833	1.0382	-0.3116	-0.1278	0.1133	0.2782	-0.034	-0.0964	0.4545	0.0373	0.3884	37.3431	35.9249	54.69
16	0.0879	-0.0093	-0.1356	1.7707	2.0287	4.6453	-0.1189	0.1845	0.144	-0.145	0.0288	0.2474	-0.2221	0.0268	0.1041	0.2527	-0.041	-0.0531	0.3889	0.0456	0.3621	41.9071	34.283	64.3137
17	0.5823	-0.8662	0.1988	1.514	0.0059	1.2548	-0.0566	0.1477	0.1214	0.04	0.0439	-0.1102	-0.0256	0.0894	0.0119	0.2253	-0.0623	-0.0232	0.3853	0.0224	0.3146	50.4906	30.7837	72.1067
18	1.1311	0.2072	0.3508	1.4535	0.0166	2.2227	-0.0261	-0.0116	0.2108	0.1098	0.03	0.1515	-0.2226	-0.1749	-0.0229	0.2043	-0.0329	-0.0238	0.2633	0.0425	0.3221	40.6663	38.0868	78.6508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 306 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 5 through 109 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 110 through 257 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 258 through 306 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 8 through 94 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 105 through 141 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 142 through 193 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 194 through 306 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 5 through 84 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 85 through 306 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 8 through 118 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 119 through 306 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 10 through 27 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 28 through 78 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 79 through 141 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 142 through 193 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 194 through 306 )

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi