PDB-5hva: Crystal structure of DR2231 in complex with dUMPNPP and magnesium.

ID or keywords:

Entry

Database: PDB / ID: 5hva

Title

Crystal structure of DR2231 in complex with dUMPNPP and magnesium.

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: 2.1 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 28, 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 ...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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hva.cif.gz	232.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5hva.ent.gz	187.8 KB	Display	PDB format
PDBx/mmJSON format	5hva.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hva_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5hva_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5hva_validation.xml.gz	27.5 KB	Display
Data in CIF	5hva_validation.cif.gz	39.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hv/5hva ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hva	HTTPS FTP

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Related structure data

Related structure data	5hwuC 5hx1C 5hylC 5hzzC 5i0jC 5i0mC 2yfcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3koc-2 3nzk-2 2yfd-1 3qi5-2 6apj-4 3m51-d 5x55-2 4rfq-d 4fw4-2 2bco-2 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

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

1

A: DR2231

C: DR2231

hetero molecules

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

2

B: DR2231

D: DR2231

hetero molecules

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

Unit cell

Length a, b, c (Å)	148.827, 77.841, 52.560
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: 15233.110 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₃P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.5 Å³/Da / Density % sol: 50.77 % / Mosaicity: 0.15 °
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: 2.1→43.56 Å / Num. obs: 35444 / % possible obs: 97.2 % / Redundancy: 3.3 % / B_iso Wilson estimate: 26.82 Å² / R_sym value: 0.07 / Net I/av σ(I): 10.217 / Net I/σ(I): 13

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.1-2.21	2	0.45	1.8	1	85.3
2.21-2.35	2.6	0.326	2.4	1	96.4
2.35-2.51	3.7	0.279	2.8	1	99.9
2.51-2.71	3.7	0.208	3.8	1	99.9
2.71-2.97	3.7	0.12	6.5	1	100
2.97-3.32	3.7	0.069	11.3	1	99.8
3.32-3.83	3.7	0.04	18.3	1	99.6
3.83-4.7	3.6	0.031	20.4	1	99.5
4.7-6.64	3.5	0.032	18.3	1	99.6
6.64-43.56	3.3	0.02	23.2	1	98.8

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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: 2YFC

2yfc

Resolution: 2.1→43.56 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 24.5

	R_factor	Num. reflection	% reflection
R_free	0.2327	3142	4.99 %
R_work	0.1768	-	-
obs	0.1796	35387	91.49 %

Solvent computation

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

Displacement parameters

B_iso max: 104.63 Å² / B_iso mean: 35.1636 Å² / B_iso min: 7.23 Å²

Refinement step

Cycle: final / Resolution: 2.1→43.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4134	0	118	458	4710
B_iso mean	-	-	24.55	41.03	-
Num. residues	-	-	-	-	540

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4390
X-RAY DIFFRACTION	f_angle_d	0.867	5963
X-RAY DIFFRACTION	f_chiral_restr	0.042	654
X-RAY DIFFRACTION	f_plane_restr	0.006	792
X-RAY DIFFRACTION	f_dihedral_angle_d	22.976	1671

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1328	0.356	76	0.2751	1823	1899	61
2.1328-2.1678	0.3279	128	0.2741	1909	2037	65
2.1678-2.2052	0.3058	93	0.2582	2060	2153	69
2.2052-2.2453	0.3106	126	0.2463	2164	2290	73
2.2453-2.2884	0.2901	104	0.2469	2382	2486	78
2.2884-2.3352	0.2281	128	0.2188	2405	2533	83
2.3352-2.3859	0.2951	156	0.2121	2741	2897	92
2.3859-2.4414	0.2347	172	0.2097	2901	3073	99
2.4414-2.5025	0.2929	152	0.2047	3014	3166	100
2.5025-2.5701	0.2483	163	0.2052	2899	3062	100
2.5701-2.6457	0.2668	162	0.1902	2954	3116	100
2.6457-2.7311	0.2737	127	0.1961	2991	3118	100
2.7311-2.8287	0.2539	138	0.181	3012	3150	100
2.8287-2.942	0.2698	168	0.179	2949	3117	100
2.942-3.0758	0.2357	160	0.168	2944	3104	99
3.0758-3.2379	0.2101	171	0.1685	2970	3141	100
3.2379-3.4407	0.2123	160	0.1624	2934	3094	99
3.4407-3.7063	0.2334	135	0.1491	2993	3128	100
3.7063-4.079	0.2085	140	0.1462	2974	3114	99
4.079-4.6686	0.173	156	0.1355	2933	3089	99
4.6686-5.8797	0.2234	176	0.156	2967	3143	100
5.8797-43.5691	0.1975	151	0.1776	2921	3072	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	0.4718	-0.159	0.1017	0.175	-0.0215	0.0219	0.0393	0.3082	-0.2106	-0.1364	-0.0482	0.1563	-0.0468	-0.3718	0	0.255	-0.0082	-0.0295	0.4179	-0.0112	0.2623	7.6062	-184.4524	14.7933
2	1.1904	-0.3695	0.2842	0.6318	-0.0666	1.3041	-0.0008	0.0275	0.1251	-0.0242	-0.0236	0.0513	-0.1038	-0.2126	-0.0005	0.1072	0.007	-0.0005	0.1073	0.0079	0.1546	19.7215	-175.8379	25.9219
3	0.3037	0.2234	-0.0241	0.18	-0.082	0.2211	0.0092	0.0449	-0.1537	0.0784	0.0777	-0.0791	0.0926	0.2976	0	0.2175	0.0384	-0.034	0.2201	-0.0291	0.1979	35.9374	-187.4815	27.1831
4	0.2265	-0.1051	0.1184	0.8192	-0.3448	0.1714	-0.451	0.3272	-0.1518	-0.0784	0.0196	-0.2697	0.1143	0.1433	-0.1063	0.3082	0.0117	-0.0362	0.2759	-0.0659	0.2016	20.995	-194.421	9.6535
5	0.5444	0.3313	0.0759	0.3384	-0.0415	0.0709	0.0201	-0.0494	-0.1974	0.1099	-0.1339	-0.1326	0.1252	0.1201	0	0.2572	0.0018	-0.0081	0.2906	0.0182	0.2482	62.289	-182.2886	11.9014
6	0.7107	-0.336	-0.0232	0.1624	0.0359	0.1241	-0.0643	-0.0492	0.2863	0.0898	-0.0461	-0.0512	-0.3896	-0.0044	-0.0019	0.2743	-0.0592	-0.0469	0.1702	-0.0017	0.2547	49.0585	-166.586	-0.4076
7	1.0381	-0.1982	0.5846	0.3836	-0.0292	0.8928	0.1378	-0.1397	-0.0737	0.0576	-0.0891	0.0029	0.1331	-0.0539	0.0003	0.1842	-0.0424	-0.0141	0.1602	0.006	0.1511	46.6316	-184.7981	3.3075
8	0.1679	-0.2041	0.1576	0.2743	-0.1792	0.1524	0.0175	-0.3474	-0.0274	0.2308	-0.0179	0.0699	0.1723	-0.1565	0.0161	0.2378	-0.062	0.0001	0.2673	0.0149	0.2244	19.6603	-187.1142	36.4289
9	0.73	0.074	-0.4623	0.0948	0.0442	0.3755	-0.0087	0.2406	0.1914	0.0033	-0.0832	0.0111	0.1749	-0.0293	-0.0041	0.2061	0.0048	-0.0196	0.1901	0.0447	0.2193	27.5859	-175.7575	17.3342
10	0.4039	0.0812	0.3023	0.0934	0.2057	0.5848	0.0606	0.0158	-0.0465	-0.0132	-0.0677	0.0513	0.0148	-0.1605	0	0.1369	-0.0056	-0.0063	0.1955	0.0005	0.1825	15.3391	-180.0955	25.2026
11	0.0464	-0.0293	0.0892	0.0972	-0.0438	0.1624	-0.0553	-0.443	0.2986	0.0237	-0.0414	0.1125	-0.1264	-0.3095	-0.0033	0.3115	0.0518	0.0014	0.5264	-0.0568	0.3215	2.0037	-173.1625	34.2453
12	0.4301	0.3761	0.3013	0.3271	0.2494	0.231	0.0274	0.2635	-0.1673	-0.1302	0.0272	-0.0493	0.2337	0.1718	-0	0.2659	0.0118	0.006	0.2533	-0.0187	0.2359	50.1933	-185.5662	-10.4125
13	0.9266	0.0575	-0.0547	0.2816	-0.3489	0.4122	0.0438	-0.1608	0.0335	0.0386	-0.0724	0.0005	0.0383	0.0854	-0	0.1596	-0.0312	-0.013	0.1545	-0.0225	0.1651	48.3412	-177.1221	5.0659
14	1.5862	-0.1917	0.5776	0.4395	0.3854	0.7061	-0.1528	0.816	0.6864	-0.1533	-0.081	0.1679	-0.406	0.363	-0.1083	0.3055	-0.1064	0.006	0.4289	0.0854	0.3143	67.3076	-170.842	-7.853

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 33 )	A	5 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 117 )	A	34 - 117
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 133 )	A	118 - 133
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 134 through 144 )	A	134 - 144
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 33 )	B	6 - 33
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 34 through 70 )	B	34 - 70
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 71 through 144 )	B	71 - 144
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 5 through 33 )	C	5 - 33
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 34 through 70 )	C	34 - 70
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 71 through 113 )	C	71 - 113
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 114 through 144 )	C	114 - 144
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 6 through 33 )	D	6 - 33
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 34 through 113 )	D	34 - 113
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 114 through 144 )	D	114 - 144

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