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

ID or keywords:

Entry

Database: PDB / ID: 8pqq

Title

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88Q Mutant bound to Clofarabine

Components

(Nucleoside 2-deoxyribosyltransferase) x 2

Keywords

PROTEIN BINDING / Complex / Transferase / Clofarabine

Function / homology

deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / Chem-CFB / Nucleoside 2-deoxyribosyltransferase

Function and homology information

Biological species

Chroococcidiopsis thermalis PCC 7203 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.23 Å

Authors

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

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	8pqq.cif.gz	270 KB	Display	PDBx/mmCIF format
PDB format	pdb8pqq.ent.gz	220.2 KB	Display	PDB format
PDBx/mmJSON format	8pqq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pqq_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8pqq_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8pqq_validation.xml.gz	26.3 KB	Display
Data in CIF	8pqq_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pq/8pqq ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pqq	HTTPS FTP

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Related structure data

Related structure data	8pqpC 8pqrC 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

A: Nucleoside 2-deoxyribosyltransferase

B: Nucleoside 2-deoxyribosyltransferase

C: Nucleoside 2-deoxyribosyltransferase

D: Nucleoside 2-deoxyribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author
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)	136.100, 136.100, 87.440
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Nucleoside 2-deoxyribosyltransferase Mass: 17819.359 Da / Num. of mol.: 3 / Mutation: E88Q 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 B (bacteria) / Strain (production host): BL21 / References: UniProt: K9TVX3
#2: Protein	Nucleoside 2-deoxyribosyltransferase Mass: 17688.162 Da / Num. of mol.: 1 / Mutation: E88Q Source method: isolated from a genetically manipulated source Details: Clofarabine Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria) Strain: PCC 7203 / Gene: Chro_1188 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21 / References: UniProt: K9TVX3
#3: Chemical	ChemComp-CFB / 2-CHLORO-9-(2-DEOXY-2-FLUORO-B -D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE / CLOFARABINE Mass: 303.677 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₁ClFN₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.29 Å³/Da / Density % sol: 62.57 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% w/v PEG 6000; 0.1 M Tris pH 8; 0.2 M Magnesium chloride hexhydrate

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.16→117.76 Å / Num. obs: 49420 / % possible obs: 100 % / Redundancy: 20.9 % / CC_1/2: 0.885 / R_merge(I) obs: 0.24 / R_rim(I) all: 0.246 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.16→2.2 Å / R_merge(I) obs: 3.741 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2448 / CC_1/2: 0.343 / R_rim(I) all: 3.832 / % possible all: 99.51

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158	phasing
PHENIX	1.19.2-4158	refinement
xia2	3.8.dev0	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.23→58.933 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2189	2132	4.74 %
R_work	0.1726	-	-
obs	0.1748	44999	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.23→58.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4981	0	82	220	5283

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5200
X-RAY DIFFRACTION	f_angle_d	0.978	7076
X-RAY DIFFRACTION	f_dihedral_angle_d	8.339	3100
X-RAY DIFFRACTION	f_chiral_restr	0.061	752
X-RAY DIFFRACTION	f_plane_restr	0.007	907

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 (%)
2.23-2.2819	0.3648	155	0.3194	2837	X-RAY DIFFRACTION	100
2.2819-2.339	0.3298	137	0.2938	2828	X-RAY DIFFRACTION	100
2.339-2.4022	0.3266	148	0.2584	2832	X-RAY DIFFRACTION	100
2.4022-2.4729	0.2928	128	0.2477	2863	X-RAY DIFFRACTION	100
2.4729-2.5527	0.2697	158	0.2366	2835	X-RAY DIFFRACTION	100
2.5527-2.644	0.3003	148	0.2274	2847	X-RAY DIFFRACTION	100
2.644-2.7498	0.2734	122	0.2115	2850	X-RAY DIFFRACTION	100
2.7498-2.875	0.2709	146	0.2022	2842	X-RAY DIFFRACTION	100
2.875-3.0265	0.2537	150	0.1961	2861	X-RAY DIFFRACTION	100
3.0265-3.2161	0.2577	138	0.1867	2852	X-RAY DIFFRACTION	100
3.2161-3.4644	0.2275	151	0.1847	2842	X-RAY DIFFRACTION	100
3.4644-3.813	0.2033	116	0.1645	2902	X-RAY DIFFRACTION	100
3.813-4.3646	0.1674	157	0.1286	2853	X-RAY DIFFRACTION	100
4.3646-5.4983	0.1633	146	0.1269	2874	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	4.2305	-0.4102	0.1017	1.6765	-0.2933	2.1948	-0.0758	-0.0117	0.2403	0.1422	0.0625	0.0734	0.1133	-0.2566	0.0378	0.425	-0.0416	-0.0303	0.454	-0.0174	0.4054	-22.4263	60.4117	-8.7118
2	5.969	-0.5687	-1.4726	1.1162	0.0837	3.6812	0.3905	0.0719	1.0969	0.1806	-0.0402	0.099	-0.3928	-0.0653	-0.238	0.3723	0.0029	0.0289	0.4361	0.0211	0.4749	-21.5537	65.2878	-7.5597
3	9.472	1.823	-6.0729	3.5152	-1.7854	7.3268	0.6381	0.2455	0.7785	0.1572	-0.2421	0.0521	-0.6951	0.03	-0.1869	0.4819	0.0096	-0.096	0.5308	-0.0402	0.6072	-8.0543	66.2529	-4.1882
4	1.5685	-0.2212	0.522	1.8881	0.4831	2.5453	0.0913	-0.0401	-0.1166	0.0781	-0.0661	0.0086	0.2058	0.0197	-0.0652	0.4363	-0.0257	-0.0207	0.4967	0.0266	0.3953	-16.5881	48.9522	-5.0628
5	4.5663	-0.8119	0.744	1.1236	-0.7797	2.4849	0.0782	-0.3691	-0.7072	0.1852	0.0708	0.333	0.1353	-0.2065	-0.1695	0.5117	-0.0716	-0.0142	0.5186	0.0656	0.6263	-19.6203	41.0478	-0.244
6	4.3023	-0.1131	-1.9779	4.5218	1.6714	5.7832	-0.0865	-0.1053	-0.399	0.401	-0.2918	0.5819	0.5591	-0.7063	0.8816	0.4392	-0.0365	0.1037	0.4493	-0.0253	0.5294	-31.9721	50.8253	2.4877
7	6.8016	-1.4094	2.0169	1.8657	-2.9014	6.4453	-0.0935	-0.13	0.0748	-0.3993	-0.065	-0.1147	-0.6797	0.5555	0.3243	0.5731	0.0221	-0.0809	0.3355	-0.0723	0.3413	-27.8152	48.0177	-41.5341
8	4.7737	-3.6262	1.1404	8.8811	2.585	3.1745	-0.1985	-0.0443	-0.3793	0.4615	0.0937	0.0973	0.5351	-0.3862	-0.0946	0.4324	-0.0137	-0.0197	0.5212	-0.0083	0.4119	-26.388	48.9159	-20.3765
9	2.4667	0.6741	1.2881	5.434	-0.8576	2.4839	0.0936	0.0101	-0.029	-0.0795	0.0751	0.5817	0.0432	-0.1141	-0.1013	0.4746	0.0087	-0.0227	0.4914	-0.0556	0.4586	-29.659	50.0247	-33.4095
10	6.14	3.6178	-5.0386	3.766	-2.6149	4.3211	0.343	-1.2688	-0.6199	0.7098	0.7067	1.6866	-0.0254	-0.9434	-0.0547	0.6738	-0.0885	-0.0719	1.0862	0.1433	1.1224	-32.5236	32.2438	-24.7136
11	1.7903	-0.8527	0.3233	3.1632	-0.2765	3.1384	0.0103	-0.0153	-0.3117	-0.0192	0.1118	0.2526	0.3302	-0.282	-0.186	0.3434	-0.0303	-0.0199	0.5213	-0.091	0.516	-21.0052	39.1859	-31.4502
12	2.4984	-0.1901	0.7959	3.4579	0.6593	1.6242	0.0531	0.3323	0.17	-0.1822	-0.0033	-0.3191	-0.085	0.2923	-0.0324	0.3864	-0.0276	0.0008	0.5687	-0.0375	0.4403	-13.147	54.1466	-35.202
13	4.1796	1.543	0.4728	1.4156	0.1972	1.3514	0.1314	0.0055	-0.6952	0.124	-0.1209	0.0301	0.4075	-0.0779	-0.1676	0.5013	0.0964	-0.1316	0.4449	0.0085	0.5385	5.7752	40.4874	-4.6424
14	1.2211	0.1112	0.3738	1.3512	-0.8017	2.7037	0.042	0.471	-0.1498	-0.1136	-0.0593	-0.5253	0.0788	0.5897	-0.1109	0.4463	0.1963	-0.1187	0.704	-0.1499	0.7305	5.3336	35.8584	-27.4576
15	2.7808	-1.2601	0.8162	4.1775	0.2729	2.0647	0.1021	0.768	0.2199	-0.3008	-0.1957	-1.5756	0.3368	0.7402	0.0303	0.4542	0.1402	-0.0518	0.8979	-0.1799	0.9454	8.3643	36.7352	-32.2725
16	3.6214	-0.0901	0.1936	7.6771	0.8269	4.5764	0.323	0.5389	0.4172	-0.5806	-0.1864	-1.0283	-0.1437	0.5445	-0.1491	0.478	0.0917	0.0638	1.0203	-0.1072	0.7227	0.6859	45.725	-39.636
17	1.9185	1.1561	1.0705	1.6177	-0.2832	4.3932	0.1159	0.1978	-0.4828	0.0004	-0.0603	-0.0248	0.1303	0.025	-0.064	0.4346	0.1077	-0.1031	0.5498	-0.1774	0.6023	-7.7575	34.4949	-26.52
18	2.3576	1.4184	1.6889	3.7667	0.9791	4.2954	0.165	-0.1775	-0.7781	0.2294	0.1586	0.3935	0.6815	-0.0503	-0.2303	0.6102	0.0368	-0.088	0.4141	-0.0221	0.6449	-12.0649	26.564	-24.2449
19	3.4198	-0.9965	-0.8342	3.0454	-2.3844	3.885	0.0437	0.1739	-1.4562	0.069	0.4854	-0.9859	1.8807	0.5865	-0.5094	0.9973	0.2626	-0.1623	0.6616	-0.2475	1.1857	-0.8407	18.1028	-30.0738
20	3.3395	0.0021	-0.068	2.3908	0.9623	1.3494	0.2804	-0.3288	-1.1418	0.3568	-0.0829	-0.0815	0.3844	-0.1341	-0.0502	0.5766	0.0449	-0.1354	0.5226	0.125	0.6725	5.0197	36.9657	0.3044
21	9.7249	3.5583	0.8716	5.4997	1.4805	4.2296	0.0019	-0.6292	-1.2274	0.1966	-0.1119	-0.4469	0.4312	-0.0211	0.0877	0.6323	0.029	-0.022	0.604	0.1861	0.6059	-7.5336	39.1779	5.8413
22	2.968	0.2207	-0.3004	2.156	-0.2713	2.2405	0.0038	0.0398	-0.1462	-0.0117	0.0003	-0.0238	0.0932	-0.1174	0.039	0.4131	0.0124	-0.0548	0.4615	-0.0002	0.4214	-0.414	51.1922	-7.399
23	2.2333	-0.3548	-0.5403	1.2764	1.5077	2.413	-0.0546	0.2493	0.3364	0.0275	0.1096	-0.1498	-0.1218	0.0039	-0.0708	0.4011	-0.0208	-0.0534	0.4956	0.056	0.5329	2.8955	60.1139	-9.4189
24	4.7443	2.0829	0.4457	2.5241	-0.9341	1.6351	0.1678	0.0311	0.1463	0.0561	-0.2147	-0.3789	-0.2685	0.0193	-0.027	0.45	0.0227	-0.1206	0.5061	0.0162	0.5631	16.0673	53.676	-3.1896

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 51 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 52 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 137 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 138 through 154 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 9 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 10 through 22 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 23 through 43 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 44 through 51 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 52 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 154 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 22 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 22 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 23 through 51 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 52 through 68 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 69 through 112 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 113 through 140 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 141 through 154 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 23 through 51 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 52 through 68 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 69 through 112 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 113 through 137 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 138 through 154 )

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