PDB-6ozg: Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89...

ID or keywords:

Entry

Database: PDB / ID: 6ozg

Title

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Components

DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)-R(P*NP*N)-D(P*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: 1.93 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 2.0	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code / _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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/6ozg ftp://data.pdbj.org/pub/pdb/validation_reports/oz/6ozg	HTTPS FTP

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Related structure data

Related structure data	6ozeC 6ozfC 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	6fj4-d 1sci-d 5ysp-2 3teb-1 4yvy-d 5zdb-2 4lxi-d 5ncj-2 4lxg-d 4bag-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
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(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)-R(P*NP*N)-D(P*T)-3')

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

hetero molecules

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

1

A: Endonuclease V

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

hetero molecules

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

2

B: Endonuclease V

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.495, 82.487, 108.569
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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: 25487.781 Da / Num. of mol.: 2 / Mutation: E89Q 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(APAPTPGPA)-R(PA)-D(PGPAPT)-R(PNPN)-D(PT)-3') Mass: 3500.255 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: 25487.781 Da / Num. of mol.: 2 / Mutation: E89Q
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(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)-R(P*NP*N)-D(P*T)-3')

Mass: 3500.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 181 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 173 / 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: 51.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 7.4, 15% w/v PEG8000

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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: Nov 25, 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: 1.93→33.14 Å / Num. obs: 42382 / % possible obs: 96.7 % / Redundancy: 1 % / B_iso Wilson estimate: 32.53 Å² / Net I/σ(I): 9.9 / Num. measured all: 42382

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique obs	Diffraction-ID	% possible all
1.93-1.97	1	2174	1	75.6
1.93-33.14	1	396	1	81.4

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Processing

Software

Name	Version	Classification
Aimless	0.5.15	data scaling
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2W35

2w35

Resolution: 1.93→33.14 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.14

	R_factor	Num. reflection	% reflection
R_free	0.2093	3960	4.92 %
R_work	0.1773	-	-
obs	0.1789	42315	96.62 %

Solvent computation

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

Displacement parameters

B_iso max: 149.89 Å² / B_iso mean: 51.4769 Å² / B_iso min: 20.12 Å²

Refinement step

Cycle: final / Resolution: 1.93→33.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3579	379	27	173	4158
B_iso mean	-	-	62.69	48.78	-
Num. residues	-	-	-	-	464

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4156
X-RAY DIFFRACTION	f_angle_d	0.874	5695
X-RAY DIFFRACTION	f_chiral_restr	0.058	620
X-RAY DIFFRACTION	f_plane_restr	0.006	658
X-RAY DIFFRACTION	f_dihedral_angle_d	20.229	2456

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9258-1.9493	0.3686	113	0.3177	1975	2088	71
1.9493-1.9739	0.3165	139	0.3167	2325	2464	82
1.9739-1.9999	0.3102	151	0.2865	2439	2590	87
1.9999-2.0273	0.2432	103	0.269	2529	2632	90
2.0273-2.0562	0.3393	145	0.2651	2678	2823	93
2.0562-2.0869	0.2794	157	0.2419	2661	2818	95
2.0869-2.1195	0.2429	134	0.2362	2820	2954	98
2.1195-2.1543	0.2856	147	0.235	2745	2892	99
2.1543-2.1914	0.262	147	0.229	2827	2974	99
2.1914-2.2313	0.2182	138	0.2187	2816	2954	100
2.2313-2.2742	0.2656	135	0.2325	2853	2988	100
2.2742-2.3206	0.279	147	0.2065	2797	2944	100
2.3206-2.371	0.1959	165	0.1938	2831	2996	100
2.371-2.4262	0.2338	145	0.1966	2841	2986	100
2.4262-2.4868	0.2604	114	0.197	2837	2951	100
2.4868-2.554	0.2641	159	0.1922	2842	3001	100
2.554-2.6292	0.2882	163	0.1936	2819	2982	100
2.6292-2.714	0.2325	142	0.1902	2783	2925	100
2.714-2.8109	0.2317	146	0.1955	2844	2990	100
2.8109-2.9234	0.1847	138	0.186	2843	2981	100
2.9234-3.0564	0.2285	163	0.1959	2830	2993	100
3.0564-3.2174	0.21	143	0.1821	2835	2978	100
3.2174-3.4188	0.227	134	0.1656	2836	2970	100
3.4188-3.6824	0.1643	139	0.1622	2829	2968	100
3.6824-4.0524	0.1613	128	0.1439	2855	2983	100
4.0524-4.6374	0.1478	149	0.1259	2806	2955	100
4.6374-5.8375	0.1948	149	0.1386	2821	2970	100
5.8375-33.1453	0.1759	127	0.1647	2682	2809	94

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	9.22	4.5369	1.2745	8.5921	-0.1131	5.1775	0.4644	-0.8701	0.7162	0.3038	-0.293	0.5272	-0.4885	0.1143	-0.1399	0.3069	-0.0097	0.0156	0.318	-0.0547	0.2592	74.22	28.3571	16.9233
2	3.7544	3.7612	-0.4656	5.1315	-1.2906	4.12	-0.1051	-0.4101	1.4454	0.0939	-0.1841	1.3906	-0.6248	-1.7275	-0.0435	0.3937	0.1099	-0.0318	0.4716	-0.0193	0.6492	63.4531	29.1822	10.4395
3	6.7279	-7.398	-1.7477	9.32	0.4012	7.4511	-0.0377	1.2101	2.4078	-1.4335	0.1951	-1.2352	-0.8634	1.4631	-0.1182	0.6807	-0.1831	-0.0418	0.6386	0.19	0.5518	82.9147	31.99	-4.5494
4	7.3781	-1.4421	1.9896	7.7503	3.6326	5.7764	-0.0507	-0.1359	-0.6158	0.4176	0.0565	0.1533	1.1436	-0.1214	0.2023	0.2944	0.0001	-0.0217	0.3361	0.0035	0.2158	83.5652	14.0927	9.6294
5	3.8401	0.7057	-1.8246	4.8093	-0.0313	6.8874	0.157	0.5351	0.3038	-0.2381	0.3927	-0.0839	0.2402	0.3205	-0.3174	0.245	0.034	-0.0612	0.5443	0.0365	0.3297	90.1644	16.8239	6.9946
6	3.0647	3.8954	-1.2693	5.081	-0.1672	2.9501	0.0495	-0.6064	-0.3721	0.33	-0.1106	-0.1812	0.0646	0.0926	0.0553	0.2403	0.0104	0.0082	0.2782	-0.0103	0.2138	74.2814	18.6356	13.7107
7	7.8748	-0.6416	-1.0542	4.1816	-4.6556	6.3183	-0.0668	-0.0529	0.4591	0.2213	-0.0868	-0.4013	-0.4111	0.7564	0.3385	0.3243	-0.04	0.0174	0.4601	-0.003	0.2741	86.4492	24.1409	5.2577
8	5.7613	1.2238	-0.5482	1.5104	2.2358	4.131	-0.1229	0.5008	0.473	-0.2568	-0.0485	0.3646	-0.2258	-0.1139	0.1956	0.3004	-0.0099	-0.0622	0.288	0.0849	0.2555	73.3722	25.3706	3.6169
9	7.4668	-1.3027	-0.6681	3.4764	-0.9475	7.1453	-0.0396	1.5663	-0.1695	-0.5577	-0.3016	0.0017	-0.0111	-0.5045	0.3721	0.4457	-0.0877	-0.1016	0.8062	-0.0155	0.3695	69.3157	17.2872	-12.4046
10	4.8815	0.6084	0.4381	3.5144	1.3749	6.87	-0.1261	1.2152	-0.1232	-0.7546	0.0629	-0.0755	-0.0555	0.4888	0.0291	0.3967	-0.0462	-0.0203	0.6663	0.0175	0.2395	78.3013	19.1058	-8.7716
11	7.9604	-5.7206	5.1598	4.6233	-4.2303	7.4539	0.4334	0.7822	-0.6717	-0.2301	-0.3703	-0.2017	0.3179	0.3593	-0.0267	0.3684	0.0228	-0.0593	0.4234	-0.101	0.4492	86.9734	8.9524	5.0006
12	7.4758	0.7754	1.1209	5.7711	1.413	4.2969	0.1752	0.7671	-0.8047	-0.1044	0.2969	-0.8264	0.5908	0.5653	-0.5119	0.477	0.0255	-0.0015	0.4131	-0.1977	0.5445	83.8379	31.7208	22.0551
13	4.0513	1.0748	0.571	8.5364	-0.7425	7.2227	0.1431	0.9641	0.1741	-0.7199	-0.1204	-1.0215	0.177	0.3683	0.0159	0.2989	-0.1051	0.0715	0.4814	-0.0396	0.3659	87.775	44.2732	23.7445
14	9.0822	-0.0843	2.1838	3.9176	-0.0006	9.4208	0.1586	-0.6911	-0.7251	0.9406	-0.2495	0.4016	1.0237	-0.2322	0.0974	0.528	-0.1374	0.0433	0.4411	-0.0184	0.3305	73.4975	36.3373	35.9441
15	7.0656	-1.2388	1.2775	1.9882	1.683	4.0451	0.422	0.103	-0.6656	0.6653	-1.1562	0.5723	0.5066	-0.6449	0.6546	0.3629	-0.1265	0.0944	0.4853	-0.037	0.4472	67.1399	40.1538	33.0261
16	5.2429	0.448	0.5072	4.4921	-0.0909	2.8907	0.4672	-0.3315	-1.6839	0.5201	-0.1623	-0.6551	0.7509	-0.2372	-0.1783	0.404	-0.0437	-0.0422	0.2119	0.035	0.5069	82.6893	32.3232	32.2995
17	8.6573	2.2678	3.0267	4.4145	3.2112	5.5921	-0.2895	0.2358	-0.2749	0.0155	0.0649	0.5838	-0.249	-0.3135	0.3509	0.255	0.0076	-0.0004	0.2606	-0.0111	0.3283	71.9796	43.1602	26.9811
18	5.7248	0.7933	3.361	5.3172	3.4793	6.2551	0.0788	0.4587	-0.4146	0.0066	0.1991	-0.4311	0.2675	0.3379	-0.2698	0.2466	-0.0275	0.0234	0.2516	0.0183	0.2497	85.5148	43.6004	28.4451
19	6.9163	1.5702	1.3057	6.4741	-0.4108	7.4135	-0.0409	-0.4349	0.6964	0.0736	0.1643	0.0785	-0.2578	-0.2115	-0.148	0.1786	-0.003	-0.0304	0.2368	0.0192	0.3401	89.1937	56.8664	40.7331
20	7.1997	1.0287	1.9797	5.3263	3.7	5.5337	-0.1023	-0.4005	0.5906	-0.0836	-0.0251	-0.1059	-0.22	-0.1033	0.0517	0.192	0.0124	-0.0099	0.2352	0.0474	0.2499	83.89	54.2429	37.3194
21	3.1918	1.1968	-2.0956	6.1781	0.2937	9.0605	-0.0207	-0.5081	0.6604	0.0055	-0.1528	0.4527	-0.2482	-0.5001	0.0559	0.1778	0.0373	-0.0312	0.3467	-0.0149	0.3061	76.0401	55.2643	36.5794
22	8.9809	5.5487	-3.0912	4.1978	-3.6471	7.4531	0.4405	-0.9894	-0.8179	2.0508	-1.0359	0.7742	1.0527	-1.2296	0.5048	0.8385	-0.3132	0.2112	0.8237	-0.0423	0.5532	69.2572	38.1251	42.0085
23	3.072	4.4965	-1.8531	7.7043	-1.0505	7.1127	-0.4869	0.588	-1.5894	-0.0213	-0.0049	-0.0233	1.7683	-0.2551	0.5438	0.6512	-0.0487	0.1051	0.4285	-0.1044	0.6265	68.1548	8.0055	3.7707
24	1.2472	-3.922	4.6784	4.1734	-9.3516	8.1464	0.0198	-0.3686	-0.468	0.0074	-0.1137	0.0812	0.3538	0.08	0.2265	0.5185	-0.0322	-0.0211	0.5485	0.1201	0.5537	89.0519	37.017	47.2252

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

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