PDB-5i0j: Crystal structure of DR2231_E47A mutant in complex with dUMP

ID or keywords:

Entry

Database: PDB / ID: 5i0j

Title

Crystal structure of DR2231_E47A mutant in complex with dUMP

Components

DR2231

Keywords

HYDROLASE / alpha helix

Function / homology

Function and homology information

nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Mota, C.S. / Goncalves, A.M.D. / de Sanctis, D.

Funding support

Portugal, 1items

Citation

Journal: FEBS J. / Year: 2016
Title: Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP.
Authors: Mota, C.S. / Goncalves, A.M. / de Sanctis, D.

History

Deposition	Feb 4, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 14, 2016	Group: Database references
Revision 1.2	Apr 4, 2018	Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5i0j.cif.gz	234.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5i0j.ent.gz	188.9 KB	Display	PDB format
PDBx/mmJSON format	5i0j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5i0j_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5i0j_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5i0j_validation.xml.gz	30.6 KB	Display
Data in CIF	5i0j_validation.cif.gz	45.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/5i0j ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i0j	HTTPS FTP

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Related structure data

Related structure data	5hvaC 5hwuC 5hx1C 5hylC 5hzzC 5i0mC 2yfcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2yfd-1 2yfc-1 3m50-d 5hx1-2 2yfc-2 5hva-2 6siq-d 3wrr-d 5hx1-1 6fc3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: DR2231

B: DR2231

C: DR2231

D: DR2231

hetero molecules

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

1

A: DR2231

D: DR2231

hetero molecules

defined by software
30.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DR2231

C: DR2231

hetero molecules

defined by software
30.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.731, 78.070, 52.439
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	DR2231 Mass: 15175.075 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_2231 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RS96
#2: Chemical	ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₈P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H₂O

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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: 51.28 % / Mosaicity: 0.14 °
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 7.5 / Details: Lithium Acetate, PEG3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.939 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.939 Å / Relative weight: 1

Reflection

Resolution: 1.8→43.531 Å / Num. obs: 57862 / % possible obs: 99.9 % / Redundancy: 5.3 % / B_iso Wilson estimate: 18.62 Å² / R_sym value: 0.107 / Net I/av σ(I): 6.636 / Net I/σ(I): 12.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.8-1.9	5.3	0.883	0.9	1	100
1.9-2.01	5.3	0.536	1.4	1	100
2.01-2.15	5.3	0.319	2.4	1	100
2.15-2.32	5.3	0.202	3.8	1	99.9
2.32-2.55	5.3	0.142	5.4	1	100
2.55-2.85	5.3	0.101	7.5	1	99.9
2.85-3.29	5.2	0.067	10.8	1	99.9
3.29-4.02	5.2	0.046	14.4	1	99.9
4.02-5.69	5	0.037	16.1	1	99.9
5.69-43.531	4.8	0.029	18.7	1	99.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdbid 2YFC

2yfc

Resolution: 1.8→43.531 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 20.17

	R_factor	Num. reflection	% reflection
R_free	0.211	5568	5.08 %
R_work	0.1731	-	-
obs	0.175	57787	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 84.24 Å² / B_iso mean: 23.6381 Å² / B_iso min: 5.27 Å²

Refinement step

Cycle: final / Resolution: 1.8→43.531 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4140	0	40	780	4960
B_iso mean	-	-	11.8	35.08	-
Num. residues	-	-	-	-	542

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4273
X-RAY DIFFRACTION	f_angle_d	0.788	5825
X-RAY DIFFRACTION	f_chiral_restr	0.042	650
X-RAY DIFFRACTION	f_plane_restr	0.006	783
X-RAY DIFFRACTION	f_dihedral_angle_d	18.581	1602

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8205	0.3219	197	0.3152	3509	3706	100
1.8205-1.8419	0.3424	179	0.3034	3469	3648	100
1.8419-1.8643	0.2832	202	0.283	3468	3670	100
1.8643-1.8879	0.3044	212	0.265	3424	3636	100
1.8879-1.9128	0.2789	164	0.2577	3497	3661	100
1.9128-1.939	0.2872	197	0.2421	3492	3689	100
1.939-1.9667	0.2984	201	0.2278	3443	3644	100
1.9667-1.996	0.2405	177	0.2126	3446	3623	100
1.996-2.0272	0.2632	184	0.2053	3472	3656	100
2.0272-2.0605	0.266	206	0.2039	3469	3675	100
2.0605-2.096	0.1988	170	0.1867	3487	3657	100
2.096-2.1341	0.2402	184	0.1852	3442	3626	100
2.1341-2.1752	0.1913	197	0.1738	3486	3683	100
2.1752-2.2196	0.214	151	0.1707	3466	3617	99
2.2196-2.2678	0.2034	185	0.1622	3479	3664	99
2.2678-2.3206	0.2027	203	0.1546	3409	3612	99
2.3206-2.3786	0.1941	189	0.1547	3535	3724	100
2.3786-2.4429	0.2325	171	0.1643	3416	3587	99
2.4429-2.5148	0.2352	165	0.1687	3549	3714	100
2.5148-2.5959	0.2323	187	0.1656	3437	3624	99
2.5959-2.6887	0.2152	178	0.1611	3480	3658	99
2.6887-2.7963	0.2133	178	0.1577	3463	3641	100
2.7963-2.9236	0.1874	213	0.149	3449	3662	99
2.9236-3.0777	0.1651	181	0.142	3473	3654	99
3.0777-3.2704	0.2049	188	0.1477	3466	3654	100
3.2704-3.5229	0.168	184	0.1431	3456	3640	100
3.5229-3.8772	0.1825	142	0.142	3486	3628	100
3.8772-4.4377	0.1518	182	0.147	3467	3649	99
4.4377-5.5892	0.2047	192	0.1641	3453	3645	99
5.5892-43.5434	0.2067	209	0.1938	3437	3646	99

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	0.0187	0.0246	-0.0276	0.0322	-0.0333	0.0275	0.0445	-0.0144	-0.0563	0.0163	0.0652	0.0385	0.0127	-0.0696	0.0264	-0.3822	-0.3945	0.1486	0.3898	0.0962	0.2311	5.5435	-37.6201	25.1917
2	0.0696	-0.0202	-0.0387	0.0752	-0.0244	0.0605	-0.0101	0.1561	-0.0995	-0.0608	-0.0842	0.058	0.0456	-0.3641	-0.0159	0.1297	-0.023	-0.031	0.3041	-0.0058	0.1529	8.1812	-27.6683	12.7579
3	0.6008	-0.0391	-0.2286	0.3245	-0.0312	0.1613	-0.0521	0.0372	0.2229	-0.0159	0.0082	-0.0547	-0.2471	-0.3598	0.0282	0.1532	0.0638	-0.021	0.0954	0.0106	0.1818	20.0427	-12.5254	23.4895
4	0.1608	0.0312	-0.0619	0.2535	-0.2377	0.1313	0.0636	-0.0516	0.0897	-0.0667	-0.0104	-0.0046	-0.2435	-0.4359	0.0659	0.0783	0.0436	-0.0099	0.1926	-0.0081	0.1144	15.083	-17.8025	29.6659
5	0.09	-0.0144	-0.1272	-0.0032	-0.0059	0.0859	0.0479	0.0678	0.0344	-0.0186	-0.0674	-0.0573	0.2277	-0.0088	-0.0011	0.1284	-0.0294	-0.0133	0.0974	0.0059	0.1255	25.7635	-34.5936	24.1771
6	0.0555	0.0775	0.0863	0.07	-0.0473	0.0899	0.0063	0.1159	-0.0924	-0.0585	0.162	-0.1282	0.023	0.2487	0.0056	0.0932	0.0106	-0.0238	0.1064	-0.026	0.0923	36.1966	-31.9109	27.127
7	0.0192	-0.0122	0.0148	0.0103	0.0046	0.0219	-0.028	0.2204	-0.1758	0.0118	-0.0072	-0.0591	-0.0048	-0.0375	-0.0027	0.2026	0.0047	-0.0325	0.1422	-0.0349	0.1066	21.3906	-39.0072	9.5509
8	0.0551	0.0359	-0.0127	-0.0018	0.0062	-0.0088	-0.0395	-0.0368	-0.1027	0.0614	0.0076	-0.0851	-0.0171	0.1818	-0	0.1199	0.0207	-0.0282	0.1727	0.0044	0.1484	65.0529	-25.7846	7.2701
9	0.0059	0.007	-0.0065	0.0094	0.0073	-0.0094	0.1275	-0.2189	-0.0967	0.0481	-0.0833	-0.0559	-0.0921	-0.0743	-0	0.2722	-0.0441	-0.0315	0.179	0.012	0.1968	58.3855	-27.1585	19.6628
10	0.1243	0.1603	-0.0031	0.0019	-0.1258	0.0196	-0.0294	-0.0591	0.1448	0.1278	-0.0084	0.0329	-0.3096	0.029	0.0144	0.1807	-0.0085	-0.0225	0.1051	-0.0157	0.1435	48.9674	-11.3926	3.0856
11	0.1596	-0.0954	0.081	0.3041	0.039	0.3907	0.0106	-0.0438	0.0381	0.012	0.0038	-0.0279	0.0703	0.072	0.0423	0.1005	-0.0138	-0.0209	0.0871	0.0085	0.1018	51.9273	-23.3183	-0.1976
12	0.0486	-0.0326	0.0435	0.0203	0.0002	0.044	0.0643	-0.0367	-0.0597	-0.0098	-0.0563	0.1362	0.0155	-0.1049	0	0.1315	-0.0385	-0.016	0.0953	-0	0.1041	33.2315	-29.9298	-6.0249
13	0.0153	0.0159	-0.0012	0.0827	-0.0366	0.0327	0.0298	-0.1931	-0.2749	0.0648	0.0713	0.0098	0.0558	-0.1797	-0.0019	0.2152	-0.0604	-0.0559	0.1392	0.0491	0.1378	45.3738	-37.8195	12.8719
14	0.0906	0.104	0.0753	0.1486	0.0561	0.0144	0.0375	0.0505	-0.0342	-0.0464	0.0264	-0.0356	0.116	0.0449	0.0253	0.1208	0.0176	-0.0124	0.0818	-0.0051	0.1143	50.043	-29.5618	-10.7572
15	0.1953	0.1024	-0.0875	0.1111	-0.0469	0.0631	0.0257	-0.0688	0.0558	0.016	0.0045	0.0522	0.0033	-0.1245	-0.0046	0.0938	-0.0134	0.0047	0.0909	-0.0126	0.0767	42.0884	-19.4157	9.001
16	0.0879	-0.0702	0.0998	0.3222	-0.0581	0.2373	0.018	-0.0086	-0.005	0.0216	-0.0474	-0.043	0.0465	0.0458	-0.0878	0.0663	-0.0212	-0.0178	0.0665	0.0064	0.0757	55.0528	-23.2237	1.6302
17	0.0113	-0.0044	-0.0075	0.0138	-0.0018	0.0081	-0.0295	0.0805	0.1021	0.1251	0.0813	-0.1891	-0.1874	0.0066	0	0.2569	-0.0472	-0.0458	0.2178	0.0158	0.2932	71.7116	-10.1783	2.6213
18	-0.0061	0.0006	-0.0012	0.0085	-0.0078	0.0073	-0.0291	0.286	0.1992	-0.0465	0.0893	-0.0512	-0.1071	0.0564	-0	0.1184	-0.0187	0.0223	0.2415	0.0348	0.1182	62.668	-18.6319	-15.2569
19	0.0994	-0.1247	0.1017	0.1581	-0.1202	0.115	0.0174	-0.2142	-0.0489	0.1492	0.0937	0.071	0.2045	-0.1967	0.0565	0.1036	-0.0541	0.0046	0.1645	0.0371	0.1324	19.9098	-31.6959	36.3797
20	0.2441	-0.0516	-0.2162	-0.0123	-0.0202	0.1004	0.0489	0.0822	0.0574	-0.0179	0.0269	-0.061	0.0069	0.0194	0.0291	0.109	0.0008	0.0006	0.0881	0.0218	0.1052	27.7291	-20.2215	17.1
21	0.1751	-0.0173	0.2322	0.1539	0.0661	0.2015	0.0605	-0.0758	0.0076	-0.0268	-0.0661	0.0127	-0.0088	-0.203	0.0159	0.0595	0.0175	-0.0025	0.1677	-0.0047	0.0917	11.2176	-22.3941	25.2277
22	0.0589	-0.0031	0.0319	-0.0005	-0.008	0.0372	-0.0779	-0.1064	0.1186	0.0848	-0.11	0.174	0.1025	-0.0583	-0.0428	0.1425	0.0841	0.0656	0.4725	-0.0312	0.1662	6.8274	-21.3659	41.3491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 9 )	A	5 - 9
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 33 )	A	10 - 33
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 63 )	A	34 - 63
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 93 )	A	64 - 93
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 94 through 117 )	A	94 - 117
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 118 through 133 )	A	118 - 133
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 134 through 144 )	A	134 - 144
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 21 )	B	7 - 21
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 22 through 33 )	B	22 - 33
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 34 through 63 )	B	34 - 63
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 64 through 112 )	B	64 - 112
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 113 through 127 )	B	113 - 127
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 128 through 144 )	B	128 - 144
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 7 through 33 )	C	7 - 33
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 34 through 69 )	C	34 - 69
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 70 through 114 )	C	70 - 114
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 115 through 133 )	C	115 - 133
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 134 through 144 )	C	134 - 144
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 5 through 33 )	D	5 - 33
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 34 through 70 )	D	34 - 70
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 71 through 133 )	D	71 - 133
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 134 through 144 )	D	134 - 144

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