PDB-8pqr: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm...

ID or keywords:

Entry

Database: PDB / ID: 8pqr

Title

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to DAD_Immucillin-H

Components

Nucleoside 2-deoxyribosyltransferase

Keywords

PROTEIN BINDING / DAD_Immucillin-H / transferase

Function / homology

deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / metal ion binding / Chem-DIH / Nucleoside 2-deoxyribosyltransferase

Function and homology information

Biological species

Chroococcidiopsis thermalis PCC 7203 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.586 Å

Authors

Tang, P. / Harding, C.J. / Czekster, C.M.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.
Authors: Tang, P. / Harding, C.J. / Dickson, A.L. / da Silva, R.G. / Harrison, D.J. / Czekster, C.M.

History

Deposition	Jul 11, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 21, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pqr.cif.gz	273.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8pqr.ent.gz	221.4 KB	Display	PDB format
PDBx/mmJSON format	8pqr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pqr_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8pqr_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8pqr_validation.xml.gz	29.1 KB	Display
Data in CIF	8pqr_validation.cif.gz	41.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pq/8pqr ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pqr	HTTPS FTP

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Related structure data

Related structure data	8pqpC 8pqqC 8pqsC 8pqtC 8qc0C 8rh3C 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

B: Nucleoside 2-deoxyribosyltransferase

A: Nucleoside 2-deoxyribosyltransferase

D: Nucleoside 2-deoxyribosyltransferase

C: Nucleoside 2-deoxyribosyltransferase

hetero molecules

71.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, The corresponding mass of ~62kDa calculated from a calibration curve of Superdex 75 Increase 10/300 GL

Unit cell

Length a, b, c (Å)	97.280, 97.280, 65.850
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Nucleoside 2-deoxyribosyltransferase Mass: 17689.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria) Strain: PCC 7203 / Gene: Chro_1188 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K9TVX3
#2: Chemical	ChemComp-DIH / 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one Mass: 265.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₇N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.52 Å³/Da / Density % sol: 51.26 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 28% v/v PEG Smear Broad; 0.1 M Tris pH 8.5; 0.15 M Ammonium Acetate; 0.01 M Calcium chloride dihydrate

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.586→51.882 Å / Num. obs: 94410 / % possible obs: 100 % / Redundancy: 10.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.121 / R_pim(I) all: 0.039 / R_rim(I) all: 0.127 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.586→1.613 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.235 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4705 / CC_1/2: 0.4 / R_pim(I) all: 1.082 / R_rim(I) all: 2.817 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
PHENIX	1.19.2-4158	phasing
autoPROC	1.0.5	data processing
autoPROC	1.0.5	data scaling
XDS	Built 20220110	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.586→51.882 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1966	4538	4.85 %
R_work	0.1701	-	-
obs	0.1714	93627	99.16 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.586→51.882 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4979	0	76	470	5525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5213
X-RAY DIFFRACTION	f_angle_d	0.922	7088
X-RAY DIFFRACTION	f_dihedral_angle_d	6.257	3412
X-RAY DIFFRACTION	f_chiral_restr	0.059	749
X-RAY DIFFRACTION	f_plane_restr	0.007	914

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 (%)
1.5861-1.6041	0.4585	109	0.4468	2547	X-RAY DIFFRACTION	84
1.6041-1.623	0.4871	148	0.4201	2747	X-RAY DIFFRACTION	93
1.623-1.6428	0.4022	136	0.3955	3000	X-RAY DIFFRACTION	98
1.6428-1.6636	0.3063	130	0.3686	2993	X-RAY DIFFRACTION	100
1.6636-1.6855	0.3751	126	0.3399	3015	X-RAY DIFFRACTION	100
1.6855-1.7086	0.3186	160	0.3148	3001	X-RAY DIFFRACTION	100
1.7086-1.733	0.3016	110	0.2949	3029	X-RAY DIFFRACTION	100
1.733-1.7589	0.3146	138	0.2764	3002	X-RAY DIFFRACTION	100
1.7589-1.7864	0.2923	154	0.2727	2968	X-RAY DIFFRACTION	100
1.7864-1.8156	0.3106	150	0.2741	2994	X-RAY DIFFRACTION	100
1.8156-1.847	0.2769	164	0.2376	2986	X-RAY DIFFRACTION	100
1.847-1.8805	0.2677	146	0.2207	3040	X-RAY DIFFRACTION	100
1.8805-1.9167	0.2473	122	0.2056	3013	X-RAY DIFFRACTION	100
1.9167-1.9558	0.196	176	0.1904	2983	X-RAY DIFFRACTION	100
1.9558-1.9984	0.2058	162	0.1835	2993	X-RAY DIFFRACTION	100
1.9984-2.0449	0.2091	160	0.1839	2959	X-RAY DIFFRACTION	100
2.0449-2.096	0.2216	202	0.1783	2993	X-RAY DIFFRACTION	100
2.096-2.1527	0.2185	136	0.1753	2964	X-RAY DIFFRACTION	100
2.1527-2.216	0.2147	146	0.1724	3024	X-RAY DIFFRACTION	100
2.216-2.2875	0.1991	144	0.1698	2982	X-RAY DIFFRACTION	100
2.2875-2.3693	0.1984	154	0.1662	3016	X-RAY DIFFRACTION	100
2.3693-2.4642	0.2003	178	0.1708	2927	X-RAY DIFFRACTION	100
2.4642-2.5763	0.2078	196	0.1697	2981	X-RAY DIFFRACTION	100
2.5763-2.7121	0.2016	172	0.1689	2955	X-RAY DIFFRACTION	100
2.7121-2.882	0.1914	180	0.1638	2996	X-RAY DIFFRACTION	100
2.882-3.1045	0.2142	110	0.1744	3022	X-RAY DIFFRACTION	100
3.1045-3.4169	0.201	122	0.1618	3019	X-RAY DIFFRACTION	100
3.4169-3.9112	0.1932	174	0.1461	3000	X-RAY DIFFRACTION	100
3.9112-4.9271	0.1485	162	0.1227	2972	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	2.4081	-0.4035	0.4365	2.6907	-3.2925	4.7488	-0.2362	-0.4423	-0.6953	-0.0381	-0.0501	-0.5977	0.6131	0.1759	0.2159	0.3709	0.0144	0.0597	0.3246	0.1172	0.4552	-10.5764	-55.5864	5.4694
2	1.5678	0.5771	0.1129	1.1117	0.5716	1.1815	0.0206	-0.1372	-0.2586	-0.0819	-0.0428	-0.2958	0.117	0.16	-0.007	0.2922	0.0175	-0.0002	0.3087	0.0667	0.3409	-2.9989	-46.5444	3.9572
3	1.5539	-0.4678	0.6124	1.3065	0.2956	1.9945	0.0521	0.0749	-0.2005	-0.1189	-0.1081	-0.173	0.1566	0.1585	0.0702	0.3322	0.01	0.019	0.2856	0.0193	0.3192	-12.4811	-48.1307	-4.0463
4	4.4001	1.5022	1.8147	0.6895	0.3018	1.2697	-0.0915	-0.2925	0.3749	-0.0714	-0.1113	0.4168	0.164	-0.4332	0.2937	0.324	0.009	0.0013	0.4255	-0.0753	0.3647	-16.9956	-30.7966	8.1018
5	2.0555	0.1199	1.1969	2.1207	-0.6926	2.3609	-0.0923	-0.4152	0.0177	0.2836	0.1353	0.141	-0.2087	-0.5692	-0.0082	0.3345	0.0325	0.0714	0.4542	0.0202	0.3054	-21.5624	-40.1726	11.6271
6	5.1148	0.4186	-1.0888	5.1665	1.6685	2.6032	0.2111	-1.1477	-0.7712	0.7916	-0.079	-0.1347	0.4374	-0.1074	0.0712	0.4334	-0.0696	-0.0018	0.4466	0.1976	0.3663	-14.5617	-52.2158	18.3856
7	1.8443	0.2146	-0.7175	1.4226	-0.5098	1.4202	0.0012	-0.3658	-0.0205	0.265	-0.161	-0.1235	0.0179	0.1574	0.1296	0.315	0.005	-0.0525	0.3133	0.0593	0.2912	4.8745	-25.7101	6.8833
8	2.2387	0.3449	-0.9388	1.3162	-1.2587	1.2714	-0.3011	-1.0067	-0.2872	0.4837	0.2141	-0.0558	-0.2489	0.1846	0.0513	0.455	0.047	-0.0473	0.5114	0.0349	0.3394	-0.1654	-18.1068	14.2856
9	8.3468	0.9732	-3.7905	1.0363	-0.0264	2.2788	0.3378	-0.673	0.482	-0.004	-0.0993	0.1013	-0.4792	0.2493	-0.1783	0.3972	0.0333	-0.0526	0.3469	-0.0587	0.3784	-6.1107	-11.4571	10.6589
10	1.8455	-0.5534	-0.235	1.5314	0.2272	1.1211	-0.0131	-0.1673	0.0518	0.0552	-0.1212	0.0434	-0.1064	0.0394	0.1306	0.3008	0.0001	-0.0103	0.289	0.0295	0.2784	-0.6866	-18.6287	-2.5805
11	0.8258	-0.9713	0.8697	1.5853	-1.2581	1.0204	-0.1029	0.0698	-0.1664	-0.0787	0.0833	0.1703	0.0163	0.0336	-0.0075	0.352	-0.0055	0.0152	0.3228	0.028	0.3395	-3.9934	-31.166	-10.9761
12	3.2142	-0.3334	-1.5289	1.6062	-0.4862	1.6271	0.0569	-0.0166	0.2042	-0.0021	-0.0452	0.0517	-0.1719	0.0105	-0.0112	0.3219	0.0009	0.0101	0.3063	0.0072	0.2715	-0.3579	-20.3913	-15.4641
13	1.6661	0.2327	0.0481	2.5529	-1.319	3.0138	-0.2309	0.1546	-0.0957	0.024	-0.0154	-0.4348	0.0371	0.2313	0.2306	0.3061	0.0078	0.0666	0.3189	0.0438	0.3828	8.3098	-26.723	-8.6277
14	5.3727	2.1424	0.4663	6.5381	0.0445	2.5451	-0.1958	0.0055	-0.5508	-0.1354	-0.0458	-1.0835	-0.1352	0.4525	0.2347	0.2999	-0.016	0.0317	0.3144	0.0671	0.4667	16.928	-21.1085	-5.7668
15	0.8169	-0.0802	0.0428	1.736	0.2338	1.5727	0.0303	-0.0701	0.093	-0.1384	-0.099	0.4527	-0.0334	-0.3184	0.0521	0.3428	0.0119	-0.1001	0.359	-0.0399	0.4483	-33.8613	-32.4073	-13.3268
16	0.7426	-0.3683	-0.4736	3.4255	0.9489	2.6057	-0.163	-0.5365	-0.0921	0.1476	-0.1462	0.8722	-0.2057	-1.2347	0.2875	0.3279	0.0698	-0.0142	0.5988	-0.0628	0.5246	-38.767	-35.564	-3.2272
17	1.8177	0.1485	0.2265	1.0181	-0.5269	1.8573	-0.0044	-0.1708	0.0834	-0.0798	0.0493	0.3632	0.0321	-0.1939	-0.049	0.2991	-0.0145	-0.0303	0.3068	-0.0182	0.3406	-27.9967	-41.2954	-5.6499
18	1.361	-0.0596	0.6981	2.602	-0.5532	1.4115	-0.0567	0.1484	0.0042	-0.3563	-0.0321	0.0308	0.1105	0.0639	0.0864	0.4041	0.0103	0.004	0.2985	-0.0273	0.2797	-20.3925	-39.8607	-20.8206
19	1.9469	1.5441	-0.3859	5.7618	-0.2192	4.5653	0.1887	-0.0332	-0.1039	-0.1679	-0.1147	0.1528	0.2987	-0.2012	-0.0003	1.0188	-0.2048	0.0294	0.4824	-0.3787	0.9528	-30.7272	-51.7033	-27.631
20	1.479	-0.2022	-0.1324	5.2909	1.0879	1.2071	0.0356	0.0209	0.2711	-0.1065	-0.198	-0.1022	-0.1623	-0.2091	0.1097	0.3877	0.0304	-0.1066	0.3012	-0.0075	0.3263	-18.4094	-9.9772	-13.1549
21	1.2365	-0.2793	-0.1959	4.5174	1.0087	1.0448	-0.0325	0.2591	0.0203	-0.6285	-0.2867	0.7011	-0.1808	-0.2099	0.2476	0.4135	0.045	-0.1514	0.3367	-0.0283	0.3397	-26.807	-13.8863	-15.8413
22	1.4887	-1.0341	0.0948	2.4029	1.7128	1.9406	0.4553	1.0393	0.0534	-0.6974	-0.4881	0.2306	-0.5979	-0.1447	-0.0107	0.5231	0.0659	-0.0812	0.4856	0.0011	0.3743	-13.9404	-11.3046	-21.9471
23	2.1129	-1.0087	-1.0247	1.5354	0.8188	1.3102	0.1437	0.0684	0.2283	-0.2274	-0.1037	-0.1791	-0.368	0.0317	-0.0334	0.344	0.0046	-0.05	0.2688	0.0373	0.279	-8.2189	-10.5929	-15.4681
24	4.9049	0.597	-0.9962	2.5264	-0.094	3.875	-0.1848	-0.1173	-0.8493	0.4067	-0.1897	0.022	0.2189	-0.0358	0.288	0.3281	0.011	0.0016	0.3025	-0.0381	0.3996	-17.5723	-22.3795	-4.0803
25	1.9231	-0.4119	-0.5907	1.0245	-0.582	0.7998	-0.0809	0.2261	0.0775	-0.2931	-0.0429	-0.1028	-0.0622	0.0751	0.1444	0.3524	0.0269	-0.0403	0.2871	-0.0183	0.2906	-12.1142	-10.4621	-4.4997
26	2.7834	1.0613	1.6629	0.3946	0.6288	0.9783	0.1807	-0.2837	-0.0514	0.1329	0.0136	-0.0403	-0.0296	-0.3078	-0.0579	0.3371	0.0257	-0.014	0.3386	-0.0954	0.4057	-21.9561	-22.6785	3.1387
27	1.9235	-0.8137	-0.196	2.1626	0.8278	1.1504	-0.0366	-0.0401	-0.1742	0.2296	0.0286	-0.176	0.151	0.054	0.0567	0.3775	0.0381	0.0332	0.3116	-0.0363	0.2922	-15.7236	-13.0984	7.806
28	1.6333	0.6344	0.8124	2.3794	0.6611	3.2177	-0.166	-0.1643	0.2653	0.0782	-0.1389	0.4057	-0.0187	-0.2703	0.2655	0.3436	0.0699	-0.031	0.3352	-0.0817	0.4141	-26.1174	-10.2386	0.8734
29	3.9269	0.773	-0.6499	6.6189	-0.3003	1.8491	0.1096	-0.0975	0.4619	-0.3171	-0.2584	0.9582	-0.3805	-0.2538	0.1282	0.394	0.0783	-0.1062	0.3184	-0.0651	0.462	-27.1491	-0.0413	-1.8998

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 2 through 9 )	B	A	2 - 9	1 - 8
2	2	chain 'B' and (resid 10 through 43 )	B	A	10 - 43	9 - 42
3	3	chain 'B' and (resid 44 through 102 )	B	A	44 - 102	43 - 101
4	4	chain 'B' and (resid 103 through 112 )	B	A	103 - 112	102 - 111
5	5	chain 'B' and (resid 113 through 140 )	B	A	113 - 140	112 - 139
6	6	chain 'B' and (resid 141 through 155 )	B	A	141 - 155	140 - 154
7	7	chain 'A' and (resid 2 through 33 )	A		2 - 33
8	8	chain 'A' and (resid 34 through 51 )	A		34 - 51
9	9	chain 'A' and (resid 52 through 68 )	A		52 - 68
10	10	chain 'A' and (resid 69 through 102 )	A		69 - 102
11	11	chain 'A' and (resid 103 through 112 )	A		103 - 112
12	12	chain 'A' and (resid 113 through 129 )	A		113 - 129
13	13	chain 'A' and (resid 130 through 140 )	A		130 - 140
14	14	chain 'A' and (resid 141 through 155 )	A		141 - 155
15	15	chain 'D' and (resid 2 through 33 )	D		2 - 33
16	16	chain 'D' and (resid 34 through 51 )	D		34 - 51
17	17	chain 'D' and (resid 52 through 102 )	D		52 - 102
18	18	chain 'D' and (resid 103 through 152 )	D		103 - 152
19	19	chain 'D' and (resid 153 through 153 )	D		153
20	20	chain 'C' and (resid 2 through 15 )	C		2 - 15
21	21	chain 'C' and (resid 16 through 33 )	C		16 - 33
22	22	chain 'C' and (resid 34 through 51 )	C		34 - 51
23	23	chain 'C' and (resid 52 through 75 )	C		52 - 75
24	24	chain 'C' and (resid 76 through 82 )	C		76 - 82
25	25	chain 'C' and (resid 83 through 102 )	C		83 - 102
26	26	chain 'C' and (resid 103 through 112 )	C		103 - 112
27	27	chain 'C' and (resid 113 through 129 )	C		113 - 129
28	28	chain 'C' and (resid 130 through 140 )	C		130 - 140
29	29	chain 'C' and (resid 141 through 155 )	C		141 - 155

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