PDB-6ozf: Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D11...

ID or keywords:

Entry

Database: PDB / ID: 6ozf

Title

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Components

DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')
Endonuclease V

Keywords

HYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination

Function / homology

Function and homology information

deoxyribonuclease V / deoxyribonuclease V activity / RNA endonuclease activity, producing 5'-phosphomonoesters / single-stranded RNA binding / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Samara, N.L. / Yang, W.

Citation

Journal: Mol.Cell / Year: 2019
Title: Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Authors: Wu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.

History

Deposition	May 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2	Oct 11, 2023	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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6ozf_validation.pdf.gz	283.1 KB	Display	wwPDB validaton report
Full document	6ozf_full_validation.pdf.gz	283.1 KB	Display
Data in XML	6ozf_validation.xml.gz	1.5 KB	Display
Data in CIF	6ozf_validation.cif.gz	8.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/6ozf ftp://data.pdbj.org/pub/pdb/validation_reports/oz/6ozf	HTTPS FTP

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Related structure data

Related structure data	6ozeC 6ozgC 6ozhC 6oziC 6ozjC 6ozkC 6ozlC 6ozmC 6oznC 6ozoC 6ozpC 6ozqC 6ozrC 6ozsC 2w35S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xa7-d 5erl-4 5zdd-d 5zdc-5 5equ-1 5iqv-3 3qun-d 3m96-d 5ekm-d 6yzx-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
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Endonuclease V

B: Endonuclease V

C: DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')

D: DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')

hetero molecules

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

1

A: Endonuclease V

C: DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')

hetero molecules

defined by software
Evidence: gel filtration
29.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Endonuclease V

D: DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.129, 75.578, 106.397
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein / DNA/RNA hybrid , 2 types, 4 molecules ABCD

#1: Protein	Endonuclease V / Deoxyinosine 3'endonuclease / Deoxyribonuclease V / DNase V Mass: 25634.957 Da / Num. of mol.: 2 / Mutation: D110N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nfi, TM_1865 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2H9, deoxyribonuclease V
#2: DNA/RNA hybrid	DNA/RNA (5'-D(PAPAPTPGPI)-R(PA)-D(PGPAPTPGPCPT)-3') Mass: 3727.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#1: Protein

Endonuclease V / Deoxyinosine 3'endonuclease / Deoxyribonuclease V / DNase V

Mass: 25634.957 Da / Num. of mol.: 2 / Mutation: D110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermotoga maritima (bacteria) / Gene: nfi, TM_1865 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9X2H9, deoxyribonuclease V

#2: DNA/RNA hybrid

DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')

Mass: 3727.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 341 molecules

#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.12 Å³/Da / Density % sol: 42.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M calcium acetate, 10% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2013
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 47534 / % possible obs: 99.3 % / Redundancy: 4.5 % / Net I/σ(I): 15
Reflection shell	Resolution: 1.8→1.83 Å / Num. unique obs: 2329

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2W35

2w35

Resolution: 1.8→28.093 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4

	R_factor	Num. reflection	% reflection
R_free	0.1977	2334	4.92 %
R_work	0.167	-	-
obs	0.1685	47481	99.14 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→28.093 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3585	462	39	330	4416

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4302
X-RAY DIFFRACTION	f_angle_d	1.041	5927
X-RAY DIFFRACTION	f_dihedral_angle_d	21.684	2531
X-RAY DIFFRACTION	f_chiral_restr	0.067	645
X-RAY DIFFRACTION	f_plane_restr	0.006	674

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 (%)
1.8002-1.8369	0.2963	145	0.2565	2542	X-RAY DIFFRACTION	97
1.8369-1.8769	0.2324	148	0.2341	2564	X-RAY DIFFRACTION	98
1.8769-1.9205	0.2438	157	0.2054	2564	X-RAY DIFFRACTION	98
1.9205-1.9685	0.2595	134	0.2004	2629	X-RAY DIFFRACTION	99
1.9685-2.0217	0.2418	144	0.1962	2605	X-RAY DIFFRACTION	99
2.0217-2.0812	0.2495	146	0.1915	2600	X-RAY DIFFRACTION	99
2.0812-2.1484	0.2226	132	0.1784	2652	X-RAY DIFFRACTION	99
2.1484-2.2251	0.2127	111	0.171	2660	X-RAY DIFFRACTION	99
2.2251-2.3142	0.2031	135	0.1682	2623	X-RAY DIFFRACTION	99
2.3142-2.4194	0.1966	137	0.1673	2680	X-RAY DIFFRACTION	99
2.4194-2.5469	0.2286	144	0.1766	2619	X-RAY DIFFRACTION	99
2.5469-2.7064	0.1957	132	0.1857	2682	X-RAY DIFFRACTION	100
2.7064-2.9151	0.212	135	0.1831	2685	X-RAY DIFFRACTION	100
2.9151-3.2081	0.2188	119	0.1723	2700	X-RAY DIFFRACTION	100
3.2081-3.6715	0.169	142	0.144	2718	X-RAY DIFFRACTION	100
3.6715-4.6223	0.136	143	0.1299	2734	X-RAY DIFFRACTION	100
4.6223-28.0962	0.1928	130	0.1537	2890	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	9.7267	3.0129	1.6185	2.5955	0.2633	0.2478	0.132	-0.3318	0.2144	0.2782	-0.2641	0.2241	-0.0896	-0.1819	0.1147	0.256	-0.0093	0.0157	0.2137	-0.0734	0.2203	73.6936	28.1221	15.1331
2	3.4758	1.8898	1.8839	3.6813	-2.442	5.9453	-0.0579	-1.0046	1.0244	0.1054	-0.9329	0.8598	-0.852	-1.614	0.0601	0.1917	0.285	-0.138	0.0257	-0.1164	0.5529	62.4586	29.1554	8.5313
3	5.6944	-4.3424	4.2065	6.5395	-2.0852	5.0121	0.0791	1.9353	1.2401	-1.1127	-0.2686	-0.6883	-0.5785	0.3513	-0.0291	0.6068	-0.094	0.0054	0.3215	0.0805	0.411	81.9527	30.6873	-6.6098
4	8.0573	1.2935	-1.0582	7.0906	-0.6544	7.0389	-0.0351	-0.2899	-0.2347	0.0319	0.0964	0.2818	0.7144	0.1271	-0.0782	0.1345	-0.0042	-0.026	0.1552	-0.0149	0.1206	82.3818	13.7465	7.9173
5	8.1661	0.1053	-1.1467	2.8119	1.5609	5.7708	0.1117	-0.0378	0.0704	-0.0631	0.1449	-0.1295	0.2671	0.7809	-0.1922	0.1456	0.0209	-0.0349	0.1226	-0.0216	0.1492	89.2161	16.028	5.7068
6	8.2729	5.1764	-0.1564	3.6202	0.1171	0.2951	0.2823	-0.5528	-0.1529	0.2846	-0.2574	-0.0536	0.1021	-0.0113	-0.067	0.1245	-0.0041	0.009	0.1626	-0.0271	0.1242	73.2676	18.4595	12.3519
7	5.615	2.5213	1.1185	7.7069	-1.1997	7.6722	-0.3204	0.4612	0.1396	-0.161	0.3484	-0.4156	-0.3105	0.456	0.0477	0.1025	0.02	0.0306	0.1231	-0.0214	0.1319	85.2601	22.7743	3.7099
8	2.8326	0.1679	0.6446	1.5961	1.1143	2.8127	-0.2613	0.016	0.3878	-0.2573	-0.0082	0.4106	-0.386	-0.0775	0.2538	0.1723	0.0146	-0.0562	0.1199	0.0234	0.1865	72.4001	24.7344	2.0075
9	5.607	-0.394	-0.8799	3.4234	-0.335	8.2694	-0.1925	1.0196	0.0418	-0.6808	-0.1099	0.236	-0.1775	-0.1248	0.2225	0.296	-0.0707	-0.1157	0.3454	0.0337	0.2306	67.9258	16.1924	-13.5469
10	2.8739	1.2482	1.2355	2.3454	0.6744	3.505	-0.2522	0.6728	0.1331	-0.5094	0.1764	0.0722	-0.1494	0.2584	0.0339	0.2514	-0.0681	-0.0242	0.282	0.0492	0.1323	76.9643	17.6386	-10.0168
11	7.6894	-0.9307	3.4209	7.183	-5.1667	8.4722	0.0227	0.1536	-0.384	0.1249	-0.0591	-0.4911	0.1901	0.1268	-0.017	0.1672	0.0279	-0.0291	0.1535	-0.0436	0.1916	85.4813	8.445	4.0339
12	3.1211	-2.3161	1.7546	5.016	-0.4965	3.368	-0.0754	0.5692	-0.3193	0.1465	-0.0007	-0.2117	0.2313	0.4037	0.0038	0.2149	0.0476	-0.0158	0.232	-0.0547	0.1967	84.0729	30.5509	19.9208
13	2.3312	-0.3138	-1.1978	4.5462	-0.4887	3.605	0.3801	0.636	0.3573	-0.5334	-0.3465	-0.4647	-0.0331	-0.0517	0.0167	0.1515	-0.0297	-0.0077	0.2424	-0.0182	0.0917	88.2675	43.1013	22.5446
14	6.6292	-1.9655	1.3564	6.1615	-0.962	5.6432	-0.1365	-0.0728	-0.5416	0.3968	-0.0987	0.1628	0.3503	-0.0051	0.1624	0.1442	-0.0137	0.0279	0.1546	-0.0253	0.1518	73.802	33.8512	34.126
15	5.8146	-2.411	-0.0014	6.1342	1.9456	2.4216	0.1067	0.3168	-0.5836	-0.0297	-0.477	0.9034	0.1901	-0.1616	0.2751	0.116	-0.031	0.0002	0.2316	-0.0681	0.2202	67.4776	37.9756	31.577
16	7.1452	-0.2819	3.967	2.5768	0.4795	3.9026	0.2134	0.0539	-0.7181	0.1525	-0.0763	0.0563	0.445	-0.0801	-0.1438	0.1832	0.0014	0.0201	0.1512	-0.0246	0.1725	82.8998	30.3401	29.9702
17	6.8605	3.0196	3.1642	7.1591	-0.5315	8.5357	-0.121	0.3259	-0.1131	-0.2055	-0.1908	0.4758	-0.1551	-0.2114	0.3089	0.1543	0.0498	-0.0055	0.1758	-0.0899	0.1663	72.3473	41.438	26.5558
18	3.7757	-0.8493	-0.0613	3.1257	1.389	3.6197	0.0597	0.0564	-0.1212	-0.1947	-0.077	-0.088	-0.0164	-0.0156	0.0277	0.1154	-0.0071	0.0073	0.1098	0.025	0.0989	85.9492	42.0226	27.1788
19	6.3195	-0.9268	-0.2112	6.8476	1.6115	2.5518	0.0299	-0.0985	0.523	-0.1278	0.2046	-0.1812	-0.1552	0.0635	-0.2045	0.1003	-0.0295	-0.0166	0.1642	0.0063	0.1353	89.422	53.6086	40.7942
20	2.3386	-0.1887	0.8031	2.3542	1.5338	3.3927	0.0199	-0.0373	0.1911	-0.1437	-0.0237	-0.0065	-0.2051	0.0567	0.0051	0.0842	-0.01	0.0012	0.1149	0.017	0.1255	84.2597	51.5201	37.149
21	5.1737	-0.0999	-3.7994	2.0786	-0.1258	7.0052	0.1324	0.1074	0.2678	-0.0765	-0.0563	0.2544	-0.4365	-0.1823	-0.1039	0.1332	0.0154	-0.028	0.1105	-0.0166	0.1662	76.4795	52.8334	36.2088
22	5.24	3.269	-0.1879	3.3114	-2.6618	5.012	0.1003	-0.3295	-0.1983	0.2498	-0.2706	0.4655	0.2974	-0.5266	0.0731	0.208	-0.0569	0.0712	0.3006	-0.0209	0.2312	70.1106	35.2282	40.5874
23	1.9297	-0.115	-0.3773	6.6795	-3.9051	1.6839	-0.1239	-0.0137	-0.4731	-0.1612	0.0412	0.3832	0.6417	-0.1177	0.0807	0.2911	-0.0194	0.0405	0.2347	-0.058	0.2349	66.9304	4.7644	4.7608
24	0.8245	-3.3705	3.4273	2.1833	-7.2047	7.1563	-0.2152	-0.6462	-0.2789	0.3491	0.1973	-0.1114	-0.1661	0.1153	0.0889	0.2935	0.0426	-0.0237	0.3653	0.0302	0.2565	88.9937	33.6817	47.0089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 37 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 38 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 75 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 76 through 99 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 100 through 110 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 111 through 138 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 139 through 163 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 164 through 207 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 208 through 221 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 12 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 13 through 37 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 38 through 60 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 61 through 75 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 76 through 99 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 100 through 110 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 111 through 138 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 139 through 163 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 164 through 188 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 189 through 207 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 208 through 224 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 2 through 12 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 1 through 12 )

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