PDB-5hyl: Crystal structure of DR2231_E47A mutant in complex with dUMPNPP a...

ID or keywords:

Entry

Database: PDB / ID: 5hyl

Title

Crystal structure of DR2231_E47A mutant 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: 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 1, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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	5hyl.cif.gz	248.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5hyl.ent.gz	199.7 KB	Display	PDB format
PDBx/mmJSON format	5hyl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hyl_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5hyl_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5hyl_validation.xml.gz	33.1 KB	Display
Data in CIF	5hyl_validation.cif.gz	50.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyl ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyl	HTTPS FTP

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Related structure data

Related structure data	5hvaC 5hwuC 5hx1C 5hzzC 5i0jC 5i0mC 2yfcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hzz-1 3g58-1 6ftw-1 6d4s-d 5ahl-d 3dyn-1 6cwx-d 6d4w-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

66.4 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
33.2 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
33.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.063, 77.822, 52.713
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: 16363.429 Da / Num. of mol.: 4 / Mutation: E47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Gene: DR_2231 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RS96
#2: Chemical	ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₃P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.48 Å³/Da / Density % sol: 50.4 % / Mosaicity: 0.1 °
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: ID29 / Wavelength: 0.976 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.976 Å / Relative weight: 1

Reflection

Resolution: 1.8→43.037 Å / Num. all: 57191 / Num. obs: 57191 / % possible obs: 99.2 % / Redundancy: 4.6 % / B_iso Wilson estimate: 19.71 Å² / R_pim(I) all: 0.027 / R_rim(I) all: 0.059 / R_sym value: 0.052 / Net I/av σ(I): 9.435 / Net I/σ(I): 17 / Num. measured all: 264780

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.8-1.9	4.7	0.242	3.2	38874	8236	0.123	0.273	0.242	5.4	99.1
1.9-2.01	4.6	0.162	4.7	35785	7807	0.083	0.183	0.162	7.7	99.3
2.01-2.15	4.8	0.113	6.7	35478	7338	0.056	0.126	0.113	11.2	99.4
2.15-2.32	4.6	0.083	8.8	31716	6875	0.043	0.094	0.083	14.5	99.5
2.32-2.55	4.7	0.068	10.4	29677	6342	0.034	0.076	0.068	17.6	99.1
2.55-2.85	4.7	0.057	12	27255	5757	0.029	0.064	0.057	20.9	99.2
2.85-3.29	4.5	0.045	14.3	22689	5097	0.023	0.051	0.045	26.2	99
3.29-4.02	4.6	0.038	15.9	19862	4346	0.019	0.043	0.038	33	99.2
4.02-5.69	4.4	0.034	15.9	14990	3419	0.018	0.039	0.034	32.9	98.8
5.69-43.037	4.3	0.028	15.5	8454	1974	0.015	0.032	0.028	31.3	98.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX		refinement
SCALA	3.3.21	data scaling
PHASER		phasing
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YFC

2yfc

Resolution: 1.8→43.037 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 20.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2051	5356	4.92 %
R_work	0.1603	103549	-
obs	0.1625	57115	99.16 %

Solvent computation

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

Displacement parameters

B_iso max: 91.29 Å² / B_iso mean: 26.0293 Å² / B_iso min: 8.09 Å²

Refinement step

Cycle: final / Resolution: 1.8→43.037 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4320	0	58	913	5291
B_iso mean	-	-	23.59	35.53	-
Num. residues	-	-	-	-	566

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4507
X-RAY DIFFRACTION	f_angle_d	0.82	6147
X-RAY DIFFRACTION	f_chiral_restr	0.041	682
X-RAY DIFFRACTION	f_plane_restr	0.007	827
X-RAY DIFFRACTION	f_dihedral_angle_d	21.573	1707

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	0.2861	178	0.2372	3473	3651	98
1.8205-1.8419	0.2958	186	0.2231	3445	3631	100
1.8419-1.8643	0.2389	174	0.2051	3427	3601	100
1.8643-1.8879	0.2363	180	0.1951	3476	3656	98
1.8879-1.9128	0.2749	162	0.1986	3484	3646	100
1.9128-1.939	0.2334	191	0.1956	3406	3597	99
1.939-1.9667	0.2612	196	0.1878	3405	3601	98
1.9667-1.996	0.2389	175	0.184	3511	3686	100
1.996-2.0272	0.2392	176	0.1811	3457	3633	99
2.0272-2.0605	0.2243	180	0.1748	3390	3570	100
2.0605-2.096	0.237	147	0.1667	3550	3697	100
2.096-2.1341	0.2206	197	0.1685	3452	3649	99
2.1341-2.1751	0.2194	165	0.1699	3488	3653	100
2.1751-2.2195	0.2173	167	0.1629	3437	3604	100
2.2195-2.2678	0.1937	194	0.1539	3422	3616	99
2.2678-2.3206	0.198	209	0.1542	3422	3631	99
2.3206-2.3786	0.2232	154	0.1538	3457	3611	98
2.3786-2.4429	0.181	175	0.1628	3481	3656	100
2.4429-2.5148	0.229	172	0.1689	3504	3676	100
2.5148-2.5959	0.1957	181	0.1658	3428	3609	100
2.5959-2.6887	0.2501	168	0.167	3449	3617	99
2.6887-2.7963	0.2192	181	0.1682	3489	3670	99
2.7963-2.9236	0.2276	179	0.1557	3443	3622	99
2.9236-3.0777	0.1767	203	0.1561	3393	3596	99
3.0777-3.2704	0.1952	204	0.154	3416	3620	99
3.2704-3.5228	0.1898	169	0.1438	3507	3676	99
3.5228-3.8771	0.1925	199	0.1355	3396	3595	99
3.8771-4.4377	0.1635	172	0.1316	3438	3610	98
4.4377-5.5891	0.1669	170	0.1435	3452	3622	99
5.5891-43.0492	0.1878	152	0.1679	3451	3603	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	0.0525	0.0269	0.0416	0.0254	-0.0019	0.0219	0.0645	-0.1474	-0.1941	0.1187	-0.1877	-0.0474	-0.035	0.111	-0.0001	0.1685	-0.029	-0.0294	0.2147	0.0218	0.1456	-12.0557	-26.5082	-14.784
2	0.1863	-0.0095	0.0324	0.0628	-0.0236	0.0132	0.0487	-0.0346	0.2799	0.0553	-0.1306	0.077	-0.1231	0.0532	0.0093	0.1961	-0.0826	-0.0194	0.1142	-0.0339	0.1771	-25.5227	-10.7721	-26.981
3	0.3399	-0.1574	0.2012	0.1282	0.0665	0.222	0.0857	-0.0827	-0.0337	0.0694	-0.0583	0.0111	0.0783	-0.0334	-0.0018	0.1532	-0.0503	-0.0304	0.1141	0.0237	0.1064	-27.8617	-28.9829	-23.134
4	0.0549	-0.0087	0.0463	0.0277	-0.0126	0.007	0.0802	0.1561	-0.1241	-0.0637	-0.0563	0.0571	0.0531	-0.2002	0	0.136	-0.0207	-0.0178	0.2552	-0.0067	0.1596	-66.8717	-28.3708	-11.6918
5	0.7295	0.0527	-0.1144	0.1452	-0.0423	0.0301	-0.2054	0.6094	0.5766	-0.0203	0.1765	-0.1457	-0.2057	-0.3217	0.0036	0.1356	0.1309	-0.0691	-0.2081	0.0304	0.2848	-54.6747	-12.1105	-2.3786
6	0.111	0.0412	-0.0677	0.1215	-0.1061	0.1093	-0.0562	-0.0545	0.1534	0.0187	0.0131	0.0041	-0.0482	-0.2116	0.0104	0.1146	0.0424	-0.0373	0.147	-0.0278	0.1481	-59.5821	-17.5221	3.6605
7	0.0252	0.0151	-0.0204	0.0004	-0.0131	0.0163	0.0143	0.1575	-0.0528	0.0614	-0.0361	0.0273	0.1179	-0.0051	-0.0001	0.1357	-0.018	-0.0277	0.1	-0.0137	0.148	-51.7317	-34.6544	-4.4326
8	0.0462	0.0288	0.0273	0.0149	-0.03	0.032	0.0825	0.0233	-0.0962	-0.0227	0.0183	-0.1158	0.0059	0.0841	0.0015	0.1242	0.0057	-0.0275	0.1002	-0.0186	0.1387	-38.3082	-31.9003	2.4088
9	-0.0025	0.0007	-0.001	-0.0017	0.0016	0.0011	-0.0103	0.2138	-0.1348	-0.053	-0.056	-0.0427	0.0658	-0.2115	0	0.1943	-0.0027	-0.0355	0.2059	-0.0715	0.1597	-53.3798	-38.7094	-16.4871
10	-0.0043	-0.0056	-0.0099	-0.0007	0.0022	-0.0004	-0.0913	0.1685	-0.036	0.0849	0.073	-0.0483	-0.0096	0.0463	0	0.2355	0.0216	-0.0342	0.166	-0.0448	0.2828	-11.095	-47.3768	-35.8548
11	0.0507	0.0497	0.0357	0.0221	0.0162	0.0055	-0.0028	0.1762	-0.0347	-0.1165	0.0268	-0.0524	0.2264	0.0997	-0	0.1634	0.0116	-0.0205	0.1311	-0.0128	0.1162	-25.6647	-28.6823	-38.0438
12	0.308	0.0884	-0.0013	0.2417	-0.1023	0.0368	0.089	-0.2799	0.402	0.0938	-0.1413	0.0924	-0.0243	-0.0375	0.0087	0.1493	-0.0768	0.0114	0.2339	-0.1119	0.1154	-32.4971	-19.2911	-17.044
13	0.404	-0.0802	0.3067	0.1913	-0.0524	0.1966	0.0594	0.101	0.0429	0.0143	-0.0658	-0.0294	0.0017	0.1236	-0.0055	0.1065	-0.0304	-0.0094	0.1481	0.0117	0.1031	-14.8384	-19.9195	-28.158
14	-0.0135	-0.012	-0.0297	0.0217	-0.0534	-0.0066	-0.0876	0.0217	-0.0667	0.0158	0.0585	0.017	0.0263	0.0851	-0	0.1401	-0.0275	-0.0119	0.1039	0.023	0.1349	-57.083	-40.409	8.2158
15	0.5128	-0.2914	0.0296	-0.0015	-0.023	0.0968	0.056	0.1392	0.2152	0.0086	-0.0292	-0.0571	0.0386	-0.3082	0.0134	0.1037	-0.0197	-0.0099	0.1294	0.0331	0.1372	-48.5582	-20.8908	-3.3786
16	0.2745	-0.0194	0.2962	0.1295	0.1238	0.1508	-0.0137	-0.1218	0.0272	-0.0192	-0.0507	0.0426	-0.0573	-0.1992	-0.0214	0.0938	0.0213	-0.0134	0.1831	-0.0261	0.1118	-64.4161	-22.0217	2.1971

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 6 through 33 )	A	6 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 70 )	A	34 - 70
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 144 )	A	71 - 144
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 33 )	B	6 - 33
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 34 through 63 )	B	34 - 63
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 64 through 93 )	B	64 - 93
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 94 through 112 )	B	94 - 112
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 133 )	B	113 - 133
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 134 through 144 )	B	134 - 144
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -4 through 9 )	C	-4 - 9
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 10 through 33 )	C	10 - 33
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 34 through 70 )	C	34 - 70
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 71 through 145 )	C	71 - 145
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -4 through 21 )	D	-4 - 21
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 22 through 70 )	D	22 - 70
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 71 through 146 )	D	71 - 146

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