PDB-8swr: Structure of K. lactis PNP S42E variant bound to transition state...

ID or keywords:

Entry

Database: PDB / ID: 8swr

Title

Structure of K. lactis PNP S42E variant bound to transition state analog DADMe-IMMUCILLIN G 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

Kluyveromyces lactis NRRL Y-1140 (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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

-
Download

PDBx/mmCIF format	8swr.cif.gz	652.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8swr.ent.gz	543.1 KB	Display	PDB format
PDBx/mmJSON format	8swr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8swr_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8swr_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8swr_validation.xml.gz	58.4 KB	Display
Data in CIF	8swr_validation.cif.gz	78.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sw/8swr ftp://data.pdbj.org/pub/pdb/validation_reports/sw/8swr	HTTPS FTP

-
Related structure data

Related structure data	8swpC 8swqC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1) #145 - Jan 2012 Messenger RNA Capping 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)	89.430, 111.005, 97.870
Angle α, β, γ (deg.)	90.00, 108.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Purine nucleoside phosphorylase Mass: 33668.375 Da / Num. of mol.: 6 / Mutation: S42E 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-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG Mass: 279.295 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₁₂H₁₇N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GUN / GUANINE Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₅N₅O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.13 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% (w/v) PEG 3,350, 0.2 M di-Ammonium citrate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2013

Radiation

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

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 2.3→30 Å / Num. obs: 80600 / % possible obs: 99.9 % / Redundancy: 4.2 % / R_merge(I) obs: 0.07 / Χ²: 1.137 / Net I/σ(I): 11.9 / Num. measured all: 337016

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.3-2.34	4.2	0.823	3991	1.283	1	100
2.34-2.38	4.2	0.69	4020	1.321	1	100
2.38-2.43	4.2	0.566	4009	1.273	1	100
2.43-2.48	4.2	0.487	4004	1.293	1	100
2.48-2.53	4.2	0.414	4015	1.288	1	100
2.53-2.59	4.2	0.373	4013	1.283	1	100
2.59-2.65	4.2	0.304	4031	1.282	1	100
2.65-2.73	4.2	0.243	4030	1.246	1	100
2.73-2.81	4.2	0.202	4033	1.216	1	100
2.81-2.9	4.2	0.17	4009	1.192	1	100
2.9-3	4.2	0.131	4035	1.161	1	100
3-3.12	4.2	0.105	3996	1.083	1	100
3.12-3.26	4.2	0.088	4062	1.019	1	100
3.26-3.43	4.2	0.071	4023	0.941	1	100
3.43-3.65	4.2	0.062	4034	0.924	1	100
3.65-3.93	4.2	0.056	4058	0.931	1	100
3.93-4.33	4.2	0.05	4020	0.957	1	99.8
4.33-4.95	4.1	0.046	4061	1.044	1	99.8
4.95-6.23	4	0.04	4072	0.989	1	100
6.23-30	4.1	0.035	4084	1.009	1	98.5

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data scaling
CBASS		data collection
MOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→29.89 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2363	4038	5.02 %
R_work	0.2012	-	-
obs	0.203	80467	99.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→29.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12877	0	81	101	13059

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.638
X-RAY DIFFRACTION	f_dihedral_angle_d	5.834	1869
X-RAY DIFFRACTION	f_chiral_restr	0.042	2047
X-RAY DIFFRACTION	f_plane_restr	0.005	2319

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 (%)
2.3-2.33	0.3664	154	0.3363	2511	X-RAY DIFFRACTION	98
2.33-2.35	0.3632	128	0.32	2631	X-RAY DIFFRACTION	100
2.35-2.38	0.3502	140	0.3068	2638	X-RAY DIFFRACTION	100
2.38-2.41	0.3191	163	0.3039	2609	X-RAY DIFFRACTION	100
2.41-2.45	0.3331	139	0.2817	2623	X-RAY DIFFRACTION	100
2.45-2.48	0.3113	145	0.2712	2602	X-RAY DIFFRACTION	100
2.48-2.52	0.3042	123	0.2781	2641	X-RAY DIFFRACTION	100
2.52-2.56	0.2954	150	0.2737	2643	X-RAY DIFFRACTION	100
2.56-2.6	0.3362	126	0.259	2611	X-RAY DIFFRACTION	100
2.6-2.65	0.291	149	0.2671	2659	X-RAY DIFFRACTION	100
2.65-2.69	0.3786	124	0.2542	2642	X-RAY DIFFRACTION	100
2.69-2.75	0.3056	118	0.2547	2625	X-RAY DIFFRACTION	100
2.75-2.8	0.2907	137	0.2572	2680	X-RAY DIFFRACTION	100
2.8-2.86	0.2925	144	0.2444	2576	X-RAY DIFFRACTION	100
2.86-2.93	0.2813	158	0.2406	2614	X-RAY DIFFRACTION	100
2.93-3	0.2468	134	0.2354	2657	X-RAY DIFFRACTION	100
3-3.08	0.2958	139	0.237	2663	X-RAY DIFFRACTION	100
3.08-3.17	0.2845	153	0.2381	2599	X-RAY DIFFRACTION	100
3.17-3.28	0.2288	131	0.22	2649	X-RAY DIFFRACTION	100
3.28-3.39	0.2495	154	0.2105	2646	X-RAY DIFFRACTION	100
3.39-3.53	0.2408	143	0.2054	2631	X-RAY DIFFRACTION	100
3.53-3.69	0.2477	122	0.2018	2683	X-RAY DIFFRACTION	100
3.69-3.88	0.2185	133	0.1837	2638	X-RAY DIFFRACTION	100
3.88-4.13	0.2318	140	0.1647	2636	X-RAY DIFFRACTION	100
4.13-4.44	0.1931	134	0.1555	2657	X-RAY DIFFRACTION	100
4.44-4.89	0.1681	135	0.1448	2677	X-RAY DIFFRACTION	100
4.89-5.59	0.2064	148	0.1704	2650	X-RAY DIFFRACTION	100
5.59-7.03	0.1967	136	0.1857	2681	X-RAY DIFFRACTION	100
7.03-29.89	0.1644	138	0.1555	2657	X-RAY DIFFRACTION	98

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	3.1619	-0.1203	0.2226	2.3782	-0.6808	2.6514	0.2298	-0.738	-0.4706	0.3177	-0.3495	-0.0358	0.2975	-0.2024	0.1165	0.6428	-0.1475	-0.061	0.7858	0.1847	0.6195	71.0564	-8.7362	198.0939
2	1.8087	-0.2939	-0.2399	1.007	0.3502	2.2376	0.0327	-0.2352	0.069	0.049	-0.0403	0.0366	-0.1767	-0.5511	0.0137	0.3127	0.0147	0.0017	0.505	-0.0243	0.3336	72.6826	11.9579	190.1828
3	0.3899	0.2274	0.171	1.2365	-0.3464	2.5627	0.1324	-0.064	-0.4453	0.0815	-0.0515	-0.157	-0.0264	-0.0126	-0.0928	0.4744	0.0085	-0.052	0.757	-0.0685	0.7126	116.4733	4.5686	183.4632
4	2.8437	0.0343	0.0933	0.9648	0.1156	1.1897	0.0444	0.0237	0.2669	-0.0237	0.0599	-0.1346	-0.2245	0.1889	-0.0815	0.4073	-0.0301	0.0219	0.4134	-0.0626	0.424	101.9517	17.6036	176.4094
5	3.4026	0.0967	-0.2386	0.553	0.0587	2.4579	0.0187	0.3161	-0.0347	-0.0992	0.085	-0.0647	0.0398	-0.0949	-0.122	0.4153	0.0186	-0.0159	0.354	-0.0557	0.3578	91.9487	9.1123	168.6453
6	2.6819	0.3948	0.2066	4.7262	-0.8337	1.4987	0.1528	-0.6347	0.3027	0.569	-0.0316	-0.42	-0.2781	-0.0818	-0.0452	0.6207	-0.1021	-0.0136	0.8642	-0.2433	0.5993	94.2036	32.4775	222.7104
7	1.7382	0.7179	-0.8084	0.7031	-1.4672	3.8714	0.0547	-1.1011	0.2554	-0.4962	0.4079	-0.3559	-0.0777	0.4397	-0.0966	0.7025	-0.1379	0.197	0.3278	-0.4137	0.5921	89.779	32.0289	207.8628
8	0.3634	0.0922	0.1201	0.6925	0.2846	1.0722	0.1634	-0.4539	0.2236	-0.0303	0.0186	0.0688	-0.5685	-0.1353	-0.1892	0.6509	0.0133	0.0842	0.711	-0.1988	0.5849	82.2822	30.9597	204.3967
9	0.5848	-0.4612	-0.0226	-0.0131	0.0497	0.5955	0.2028	-0.3055	0.4319	-0.1575	0.1606	-0.2925	-0.5713	0.2666	-0.2018	0.7518	-0.098	0.1455	0.5017	-0.2584	0.7313	91.888	36.7214	198.1848
10	4.2918	-0.1187	0.4416	1.4815	0.4711	2.4347	0.1584	0.6207	-0.5115	-0.1223	-0.1515	-0.3559	0.657	0.127	0.0334	0.8745	0.1399	-0.0601	0.6193	-0.1624	0.8121	143.6654	-13.3426	219.7082
11	1.8291	-0.137	0.3203	1.2767	-0.2393	1.9441	0.0049	0.0097	-0.1955	0.0418	-0.0433	-0.1676	0.2748	0.3956	0.0367	0.3392	0.0576	-0.0325	0.4281	0.0206	0.3058	145.6847	7.5015	226.7417
12	2.0847	-0.6167	-0.138	2.8018	1.0285	2.0589	0.0582	-0.3542	-0.4743	0.0394	-0.15	0.3897	0.3825	-0.103	0.0305	0.5661	-0.1594	0.0003	0.7707	0.0258	0.6364	101.6691	6.8907	232.9251
13	3.6565	-0.6943	0.1222	1.1273	0.1477	1.071	-0.0202	-0.6155	-0.0641	0.1678	0.0567	0.073	0.1541	-0.1754	-0.0196	0.4294	-0.0918	-0.0022	0.6001	0.0564	0.3284	120.4515	16.08	242.9264
14	2.8471	-1.2221	1.4377	5.633	0.0521	2.5798	0.2276	0.7087	-0.4452	-1.564	0.1685	0.7167	0.3996	-0.063	-0.0545	0.5851	-0.0272	-0.0921	0.7746	-0.0773	0.5661	128.3332	20.515	187.8974
15	3.2969	-0.1704	1.7634	4.7422	1.7295	2.6904	-0.1525	0.3835	0.1348	-0.5421	-0.1405	0.6122	-0.4997	-0.0846	0.2146	0.5296	-0.0548	-0.0894	0.6634	0.0287	0.4886	125.4383	32.6139	193.9727
16	0.7412	-0.3729	0.1889	2.099	1.0783	3.5002	-0.1119	0.429	0.1223	-0.3057	-0.0382	0.2609	-0.2071	-0.0448	0.1106	0.3493	-0.0463	-0.0362	0.5008	0.0497	0.3878	130.0345	30.963	203.4861
17	1.4219	-0.4029	-0.0194	2.1627	0.2562	1.3136	0.023	0.1081	0.025	-0.1423	-0.0629	-0.0613	-0.0668	0.2763	-0.0076	0.3339	-0.0271	-0.0495	0.4888	0.0264	0.3343	138.3483	27.3299	211.2225
18	1.3093	-0.1131	0.4259	0.2174	0.265	1.8464	-0.0442	0.0501	0.2013	0.0705	-0.002	0.0323	-0.2204	-0.0211	0.0447	0.3531	-0.0156	-0.0056	0.3084	0.0379	0.3577	128.8271	35.281	216.9806

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 5 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 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi