PDB-8swu: Structure of Clostridium perfringens PNP bound to transition stat...

ID or keywords:

Entry

Database: PDB / ID: 8swu

Title

Structure of Clostridium perfringens PNP bound to transition state analog IMMUCILLIN H and sulfate

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

Clostridium perfringens ATCC 13124 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 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 22, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8swu.cif.gz	312.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8swu.ent.gz	254.5 KB	Display	PDB format
PDBx/mmJSON format	8swu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8swu_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8swu_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8swu_validation.xml.gz	30 KB	Display
Data in CIF	8swu_validation.cif.gz	40 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sw/8swu ftp://data.pdbj.org/pub/pdb/validation_reports/sw/8swu	HTTPS FTP

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Related structure data

Related structure data	8swpC 8swqC 8swrC 8swsC 8swtC 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

Deposited unit

A: Purine nucleoside phosphorylase

B: Purine nucleoside phosphorylase

C: Purine nucleoside phosphorylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Superdex S200

Unit cell

Length a, b, c (Å)	72.433, 91.824, 78.409
Angle α, β, γ (deg.)	90.00, 112.70, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase Mass: 29802.256 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria) Gene: punA, CPF_2818 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRIL References: UniProt: A0A0H2YR30, purine-nucleoside phosphorylase
#2: Chemical	ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H Mass: 266.253 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₄N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.69 Å³/Da / Density % sol: 54.28 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% (w/v) PEG 3,350 and 0.1 M tri-Sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.34→19.87 Å / Num. obs: 39636 / % possible obs: 99.2 % / Redundancy: 8.5 % / CC_1/2: 0.992 / R_merge(I) obs: 0.204 / R_pim(I) all: 0.073 / R_rim(I) all: 0.217 / Χ²: 1 / Net I/σ(I): 8.7 / Num. measured all: 338175
Reflection shell	Resolution: 2.34→2.43 Å / % possible obs: 93.9 % / Redundancy: 8.2 % / R_merge(I) obs: 0.756 / Num. measured all: 32293 / Num. unique obs: 3923 / CC_1/2: 0.821 / R_pim(I) all: 0.272 / R_rim(I) all: 0.806 / Χ²: 1.06 / Net I/σ(I) obs: 3.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.34→19.87 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2644	2052	5.18 %
R_work	0.2306	-	-
obs	0.2324	39580	99.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.34→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6144	0	72	38	6254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6356
X-RAY DIFFRACTION	f_angle_d	0.568	8597
X-RAY DIFFRACTION	f_dihedral_angle_d	5.155	871
X-RAY DIFFRACTION	f_chiral_restr	0.043	979
X-RAY DIFFRACTION	f_plane_restr	0.004	1106

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 (%)
2.34-2.4	0.3666	111	0.2876	2260	X-RAY DIFFRACTION	90
2.4-2.46	0.3237	132	0.271	2522	X-RAY DIFFRACTION	100
2.46-2.52	0.2898	133	0.2759	2500	X-RAY DIFFRACTION	100
2.52-2.6	0.3553	140	0.2774	2522	X-RAY DIFFRACTION	100
2.6-2.68	0.3291	141	0.278	2496	X-RAY DIFFRACTION	100
2.68-2.78	0.3287	149	0.2643	2502	X-RAY DIFFRACTION	100
2.78-2.89	0.3038	144	0.2604	2503	X-RAY DIFFRACTION	100
2.89-3.02	0.3096	169	0.2628	2493	X-RAY DIFFRACTION	100
3.02-3.18	0.2689	120	0.2646	2519	X-RAY DIFFRACTION	100
3.18-3.37	0.3041	82	0.2422	2563	X-RAY DIFFRACTION	100
3.37-3.63	0.285	114	0.2399	2552	X-RAY DIFFRACTION	100
3.63-4	0.2464	134	0.2045	2532	X-RAY DIFFRACTION	100
4-4.57	0.1933	149	0.1854	2504	X-RAY DIFFRACTION	100
4.57-5.73	0.2224	177	0.1899	2499	X-RAY DIFFRACTION	100
5.73-19.87	0.2072	157	0.1914	2561	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	2.4047	-0.7175	-0.1137	1.9366	-0.96	1.8334	-0.0942	-0.395	-0.0419	0.1699	0.1196	-0.0542	-0.0952	-0.1413	-0.0041	0.2523	0.0142	-0.0217	0.2441	-0.0256	0.2429	29.2945	-0.4615	49.1399
2	0.7142	0.0213	0.1091	0.8546	-0.1169	1.228	0.0165	-0.0918	-0.0106	0.0226	-0.0554	-0.0574	0.0668	0.0348	0.0366	0.175	-0.0148	0.001	0.1618	-0.0137	0.2208	30.9916	-6.7699	33.4417
3	2.3494	0.2892	-1.2604	1.2404	-1.0477	2.5447	0.0398	-0.2913	-0.3542	0.0161	-0.1413	0.1592	0.7571	-0.1178	0.0418	0.2523	-0.0289	0.026	0.1769	-0.0025	0.2991	24.0146	-20.982	32.1388
4	4.4664	1.8223	0.7692	3.4264	1.0127	2.6081	-0.0679	-0.0609	0.128	0.084	0.099	0.1473	0.3819	0.3203	-0.0397	0.2718	0.0779	-0.0239	0.2986	0.0403	0.3112	38.7335	-18.1026	44.0445
5	8.1902	-1.0625	2.7298	0.8958	-1.4085	2.7972	-0.0468	-0.6864	0.4965	-0.0765	-0.2901	0.4446	-0.2536	-0.7116	0.2941	0.2852	0.0573	-0.0046	0.8412	-0.129	0.4004	-7.9507	-2.0308	29.4405
6	0.7668	-0.1484	0.2212	3.4003	1.3717	2.2342	-0.0846	-0.1269	0.2948	-0.2596	-0.251	0.5962	-0.1338	-0.192	0.3535	0.2474	0.0014	-0.0816	0.4955	-0.0381	0.4608	-10.4253	-6.7454	13.7005
7	1.5016	0.5339	-0.106	0.6305	0.2095	1.1521	0.0084	0.1429	-0.1313	-0.1139	-0.0034	0.0908	0.0757	-0.2901	0.0012	0.2025	-0.005	-0.0311	0.2522	-0.0358	0.2099	8.84	-10.561	13.0769
8	1.1966	0.0129	0.457	1.3867	0.5449	0.6755	0.0725	0.3413	0.1383	-0.6211	-0.0416	0.3505	-0.0289	-0.0521	0.0026	0.4566	-0.0359	-0.1134	0.4796	-0.0573	0.3353	4.6937	-9.9767	-0.3942
9	3.558	0.7742	-1.4151	1.6907	0.2331	1.9013	0.3243	-0.0309	0.1104	-0.2348	-0.1974	-0.1095	-0.1062	0.0701	-0.0941	0.3299	0.0433	0.0101	0.2027	0.0585	0.1796	22.2233	27.9358	8.5263
10	0.202	-0.5293	-0.2429	0.9906	0.1703	-0.0556	0.0295	0.1742	0.0365	-0.1882	-0.0483	-0.0772	-0.1004	0.0178	-0.0012	0.2852	-0.009	0.0228	0.2321	0.0361	0.2115	28.7513	13.8157	7.6364
11	0.9342	0.1809	-0.4512	2.1949	-0.5331	1.2082	0.1612	0.0635	0.2004	-0.0478	-0.2652	-0.5792	-0.2371	0.3889	0.1394	0.2981	-0.029	0.0954	0.3589	0.0364	0.4167	42.4922	13.1049	8.3828

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 225 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 226 through 257 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 258 through 272 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 17 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 77 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 78 through 225 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 226 through 272 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 0 through 37 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 38 through 225 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 226 through 272 )

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