PDB-5hx1: Crystal structure of DR2231_E46A mutant in complex with dUMP and ...

ID or keywords:

Entry

Database: PDB / ID: 5hx1

Title

Crystal structure of DR2231_E46A mutant in complex with dUMP and magnesium

Components

DR2231

Keywords

METAL BINDING PROTEIN / 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: 1.799 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	Jan 29, 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 / Source and taxonomy / Structure summary Category: audit_author / entity_src_gen Item: _audit_author.name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hx1.cif.gz	234.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5hx1.ent.gz	188.6 KB	Display	PDB format
PDBx/mmJSON format	5hx1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hx1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5hx1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5hx1_validation.xml.gz	31 KB	Display
Data in CIF	5hx1_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/5hx1 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hx1	HTTPS FTP

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Related structure data

Related structure data	5hvaC 5hwuC 5hylC 5hzzC 5i0jC 5i0mC 2yfcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2yfc-1 5hwu-d 2yfc-2 2yfd-2 3et3-d 3kmg-2 4fr3-d 3cwd-1 2nom-2 5i0j-1 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

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

1

A: DR2231

C: DR2231

hetero molecules

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

2

B: DR2231

D: DR2231

hetero molecules

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

Unit cell

Length a, b, c (Å)	148.827, 77.813, 52.266
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: 14974.816 Da / Num. of mol.: 4 / Mutation: E46A 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: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.53 Å³/Da / Density % sol: 51.31 % / Mosaicity: 0 °
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: 0.976 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.976 Å / Relative weight: 1

Reflection

Resolution: 1.799→43.387 Å / Num. obs: 56414 / % possible obs: 98.6 % / Redundancy: 3.5 % / B_iso Wilson estimate: 17.21 Å² / R_sym value: 0.076 / Net I/av σ(I): 9.06 / Net I/σ(I): 12.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.799-1.9	3.1	0.447	1.7	1	97.6
1.9-2.01	3.7	0.297	2.6	1	99.8
2.01-2.15	3.7	0.185	4.1	1	99.8
2.15-2.32	3.6	0.126	6	1	99.3
2.32-2.54	3.6	0.098	7.7	1	99
2.54-2.85	3.6	0.074	10	1	98.7
2.85-3.29	3.5	0.05	13.9	1	97.7
3.29-4.02	3.4	0.036	18.4	1	97.4
4.02-5.69	3.3	0.033	17.1	1	97.4
5.69-43.387	3.3	0.022	26.3	1	97

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.16	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: 1.799→43.387 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.27

	R_factor	Num. reflection	% reflection
R_free	0.2132	2852	5.06 %
R_work	0.1731	-	-
obs	0.1752	56346	98.54 %

Solvent computation

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

Displacement parameters

B_iso max: 110.34 Å² / B_iso mean: 21.0793 Å² / B_iso min: 4.17 Å²

Refinement step

Cycle: final / Resolution: 1.799→43.387 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4095	0	44	838	4977
B_iso mean	-	-	11.72	33.41	-
Num. residues	-	-	-	-	537

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	4266
X-RAY DIFFRACTION	f_angle_d	0.793	5792
X-RAY DIFFRACTION	f_chiral_restr	0.042	648
X-RAY DIFFRACTION	f_plane_restr	0.005	782
X-RAY DIFFRACTION	f_dihedral_angle_d	17.836	1584

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7994-1.8304	0.3424	125	0.2748	2449	2574	93
1.8304-1.8637	0.28	129	0.2341	2720	2849	100
1.8637-1.8996	0.257	158	0.2058	2627	2785	100
1.8996-1.9383	0.2451	147	0.1925	2683	2830	100
1.9383-1.9805	0.2357	143	0.1823	2661	2804	100
1.9805-2.0265	0.2292	150	0.1823	2677	2827	100
2.0265-2.0772	0.2579	152	0.1857	2674	2826	100
2.0772-2.1334	0.213	150	0.1662	2660	2810	100
2.1334-2.1962	0.1888	133	0.1548	2689	2822	100
2.1962-2.267	0.2179	143	0.1531	2660	2803	99
2.267-2.3481	0.1983	131	0.1523	2687	2818	99
2.3481-2.4421	0.2135	139	0.156	2676	2815	99
2.4421-2.5532	0.2089	147	0.175	2657	2804	99
2.5532-2.6878	0.2168	138	0.1709	2696	2834	99
2.6878-2.8562	0.2275	143	0.1678	2670	2813	99
2.8562-3.0766	0.2291	136	0.1731	2691	2827	98
3.0766-3.3861	0.2104	132	0.1664	2678	2810	97
3.3861-3.8758	0.1888	144	0.16	2677	2821	97
3.8758-4.8821	0.1728	151	0.1583	2719	2870	97
4.8821-43.3997	0.2067	161	0.1949	2843	3004	97

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	0.0843	-0.0928	-0.0905	0.1084	0.073	0.0951	0.0894	0.119	-0.1251	-0.192	-0.1409	0.1328	-0.1043	-0.3016	-0.0067	0.1529	0.0101	-0.0243	0.1776	-0.0375	0.1461	12.3593	13.2222	-12.5196
2	-0.0009	-0.0582	0.0161	0.108	0.0701	0.0792	-0.0645	0.0561	0.0905	-0.1191	-0.0654	-0.0174	-0.266	0.0604	-0.0158	0.1375	0.0188	-0.0139	0.0807	-0.0052	0.0967	25.4599	27.9121	-3.072
3	0.129	0.0508	-0.0133	0.1146	-0.0133	0.1097	0.025	0.0562	0.0084	-0.0183	-0.0422	0.0375	0.1027	-0.1168	0.0155	0.0775	0.0092	-0.0168	0.0374	-0.0235	0.0632	22.7502	16.0794	0.1493
4	0.0394	0.0024	0.027	0.0055	-0.0041	0.0137	0.0389	0.0586	-0.0994	0.0821	0.0631	-0.0665	0.1538	0.1943	0.0071	0.1038	0.0162	-0.019	0.0901	0.0011	0.0792	41.3627	9.3076	5.9629
5	0.0861	0.0452	-0.0932	0.3845	-0.2047	0.1737	0.0361	0.1738	-0.1512	-0.0795	0.106	-0.0343	0.1047	0.212	0.1585	0.1511	0.0494	-0.0272	0.144	-0.0546	0.1053	29.214	1.4937	-12.8614
6	0.0264	0.0312	-0.0626	0.0333	-0.0661	0.193	-0.0885	-0.2199	-0.04	0.1109	0.1027	-0.0609	-0.1575	0.3814	0.001	0.1003	0.0202	-0.0143	0.2366	-0.0083	0.1298	68.7368	11.088	-18.8601
7	0.0162	0.0125	0.0159	0.0118	0.0142	0.0184	0.0515	-0.1093	0.0065	0.0252	0.0159	0.1175	-0.0311	0.2577	0	0.1836	-0.0349	-0.0236	0.3059	0.0012	0.1462	63.2542	11.2575	-6.89
8	0.2368	-0.0069	-0.2714	0.122	-0.0979	0.6594	-0.0289	-0.0423	0.1373	0.0037	-0.0329	0.0875	-0.1961	0.2305	-0.0174	0.1202	-0.0517	-0.0222	0.078	0.0045	0.1233	54.6364	26.8249	-23.3924
9	0.0058	-0.0081	-0.0006	0.0098	0.0007	-0.0012	-0.0904	-0.0164	-0.0162	-0.065	-0.0798	-0.0503	0.064	0.1145	-0	0.4918	-0.0457	-0.1117	0.3496	0.1426	0.3166	54.1666	30.4731	-46.0853
10	0.2142	-0.0367	-0.0666	0.0868	0.1761	0.5601	-0.0134	0.0154	0.0061	-0.0023	0.0151	-0.0418	0.0759	0.2209	-0.0218	0.0603	-0.0114	-0.0122	0.1007	0.0097	0.0785	56.5857	13.0304	-24.0799
11	0.0829	-0.0236	0.0707	0.0435	0.0147	0.0457	0.0078	-0.0864	-0.1245	-0.0059	0.1305	0.091	0.0438	-0.1754	0.0003	0.1163	-0.004	-0.0166	0.0958	0.0142	0.1179	38.1941	7.0919	-28.5494
12	0.061	0.0228	0.0459	0.205	0.0611	0.0437	-0.135	-0.1162	-0.1587	-0.0398	-0.0113	0.1109	-0.0102	0.1469	-0.0241	0.1138	0.0287	-0.0054	0.162	0.0592	0.1091	53.3415	0.2694	-9.5984
13	0.1048	-0.0671	0.077	0.0402	-0.0315	0.0233	0.0643	-0.1859	-0.1126	0.1147	-0.0253	0.1062	0.1252	-0.1198	0.0151	0.1093	-0.0204	0.0002	0.0887	-0.0042	0.1161	24.7327	10.0215	10.7858
14	0.0916	0.0131	-0.0681	0.062	0.0138	0.0463	0.0244	0.0314	0.0302	-0.0018	0.008	-0.0127	0.074	0.0344	0.0021	0.1056	0.0038	0.0031	0.0656	-0.0039	0.0775	32.5534	19.9464	-9.1431
15	0.3096	0.0023	0.1935	0.2088	-0.1045	0.2205	0.0067	-0.0601	0.0331	0.0129	-0.0309	0.0556	-0.0196	-0.0962	-0.0456	0.0667	0.0124	-0.0091	0.0678	-0.0195	0.078	15.3248	19.0576	1.5428
16	0.0944	0.0786	0.0384	0.0927	-0.0279	0.0284	0.0031	0.1985	-0.0629	-0.1668	-0.0042	-0.0726	0.1912	0.145	0.002	0.1146	0.0243	0.0069	0.1334	-0.0089	0.1034	53.9179	8.7619	-36.9302
17	0.2033	0.0915	-0.0616	0.0775	-0.0003	0.0427	0.0273	-0.0613	0.0375	0.0344	0.0395	0.0574	0.0721	-0.0445	0.0036	0.0919	0.0046	0.0106	0.059	-0.0037	0.0811	46.8019	19.0949	-16.6658
18	0.2074	-0.0716	0.1068	0.0993	-0.0057	0.0649	0.0183	-0.028	-0.0006	0.015	-0.0543	-0.0248	0.0051	0.231	-0.0579	0.0447	-0.0125	-0.0024	0.1054	0.0138	0.0599	59.4305	14.8023	-24.8893
19	0.0764	-0.0941	-0.0658	0.1248	0.0769	0.0562	0.0788	0.0758	0.2462	0.0611	0.0347	-0.1785	-0.0153	0.036	0.0235	0.1768	-0.1083	-0.0503	0.3314	0.0415	0.2628	78.1927	25.5665	-24.9888
20	0.0489	0.0441	-0.0054	0.0587	-0.0293	0.0328	-0.0577	0.1494	0.0226	-0.0962	0.0367	-0.0515	0.0416	-0.0194	-0.1107	-0.0926	-0.1616	0.1075	0.3752	-0.0192	0.1147	67.4628	18.4218	-41.5201

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 7 through 33 )	A	7 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 63 )	A	34 - 63
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 112 )	A	64 - 112
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 113 through 127 )	A	113 - 127
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 128 through 144 )	A	128 - 144
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 7 through 20 )	B	7 - 20
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 21 through 33 )	B	21 - 33
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 63 )	B	34 - 63
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 69 )	B	64 - 69
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 70 through 112 )	B	70 - 112
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 113 through 133 )	B	113 - 133
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 134 through 144 )	B	134 - 144
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 7 through 33 )	C	7 - 33
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 34 through 69 )	C	34 - 69
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 70 through 144 )	C	70 - 144
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 7 through 33 )	D	7 - 33
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 34 through 70 )	D	34 - 70
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 71 through 114 )	D	71 - 114
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 115 through 133 )	D	115 - 133
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 134 through 144 )	D	134 - 144

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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

-
Phasing

-
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