PDB-6ozr: Crystal structure of Mus musculus (Mm) Endonuclease V in complex ...

ID or keywords:

Entry

Database: PDB / ID: 6ozr

Title

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mg2+

Components

DNA/RNA (23-MER)
Endonuclease V

Keywords

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

Function / homology

Function and homology information

DNA endonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 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	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.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.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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PDBx/mmCIF format	6ozr.cif.gz	258.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ozr.ent.gz	203.5 KB	Display	PDB format
PDBx/mmJSON format	6ozr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ozr_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	6ozr_full_validation.pdf.gz	1.9 MB	Display
Data in XML	6ozr_validation.xml.gz	25.5 KB	Display
Data in CIF	6ozr_validation.cif.gz	35.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/6ozr ftp://data.pdbj.org/pub/pdb/validation_reports/oz/6ozr	HTTPS FTP

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Related structure data

Related structure data	6ozeC 6ozfC 6ozgC 6ozhC 6oziC 6ozjC 6ozkC 6ozlC 6ozmC 6oznC 6ozoC 6ozpC 6ozqC 6ozsC C: citing same article (ref.)
Similar structure data	6ozm-d 6ozq-d 6ozs-d 6p9u-1 2eiv-6 6ozl-d 3g4e-d 3g4h-d 4gnb-d 1mh0-d 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) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Endonuclease V

B: Endonuclease V

C: DNA/RNA (23-MER)

D: DNA/RNA (23-MER)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	72.078, 72.663, 154.574
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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

#1: Protein	Endonuclease V Mass: 28048.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endov / Production host: Escherichia coli (E. coli) References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: DNA/RNA hybrid	DNA/RNA (23-MER) Mass: 7293.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 296 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₆
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.09 Å³/Da / Density % sol: 60.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium sodium tartrate, 20-25% 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-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 24, 2015
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: 2.15→50 Å / Num. obs: 43769 / % possible obs: 97.3 % / Redundancy: 7.6 % / Net I/σ(I): 19.4
Reflection shell	Resolution: 2.15→2.19 Å / Num. unique obs: 1694

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→35.368 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36

	R_factor	Num. reflection	% reflection
R_free	0.1942	2198	5.03 %
R_work	0.1577	-	-
obs	0.1595	43692	97.17 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→35.368 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3814	630	84	279	4807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4865
X-RAY DIFFRACTION	f_angle_d	0.94	6727
X-RAY DIFFRACTION	f_dihedral_angle_d	16.758	2887
X-RAY DIFFRACTION	f_chiral_restr	0.055	788
X-RAY DIFFRACTION	f_plane_restr	0.005	764

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 (%)
2.1499-2.1966	0.2298	104	0.2063	2002	X-RAY DIFFRACTION	76
2.1966-2.2477	0.251	139	0.2073	2395	X-RAY DIFFRACTION	91
2.2477-2.3039	0.2533	125	0.2014	2516	X-RAY DIFFRACTION	96
2.3039-2.3662	0.2542	142	0.1885	2562	X-RAY DIFFRACTION	98
2.3662-2.4358	0.2156	126	0.1886	2662	X-RAY DIFFRACTION	99
2.4358-2.5144	0.2317	151	0.1772	2583	X-RAY DIFFRACTION	99
2.5144-2.6043	0.2121	148	0.1689	2609	X-RAY DIFFRACTION	99
2.6043-2.7085	0.217	172	0.1657	2579	X-RAY DIFFRACTION	99
2.7085-2.8317	0.2412	142	0.1745	2627	X-RAY DIFFRACTION	99
2.8317-2.9809	0.1969	115	0.1719	2678	X-RAY DIFFRACTION	99
2.9809-3.1676	0.1888	131	0.1689	2671	X-RAY DIFFRACTION	100
3.1676-3.412	0.201	148	0.1577	2650	X-RAY DIFFRACTION	100
3.412-3.755	0.2041	126	0.1484	2675	X-RAY DIFFRACTION	100
3.755-4.2975	0.1651	115	0.1276	2740	X-RAY DIFFRACTION	100
4.2975-5.4113	0.1422	157	0.1221	2711	X-RAY DIFFRACTION	100
5.4113-35.3725	0.1769	157	0.1617	2834	X-RAY DIFFRACTION	99

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	7.1424	4.3769	-3.6574	5.0195	-3.3457	3.7157	-0.1244	-0.214	-0.2466	-0.1118	-0.1326	-0.4243	0.1799	0.209	0.2782	0.1837	0.0235	0.0212	0.1021	-0.0952	0.1432	36.9195	0.8285	44.1652
2	6.9751	-0.04	-1.1394	4.396	-0.8636	7.242	-0.2053	1.1262	0.4761	-1.0334	-0.009	-0.3966	-0.4538	-0.1565	0.2244	0.4405	-0.0106	0.0195	0.3331	0.0296	0.2269	23.1693	8.4539	33.1481
3	2.1187	0.1262	-0.9379	1.2986	-0.2079	1.6972	0.0276	0.0193	0.2384	-0.0485	0.0213	-0.0172	-0.2174	-0.0288	-0.0722	0.2377	0.0017	0.0124	0.1794	-0.008	0.2046	28.0154	5.8591	40.852
4	5.1719	-1.3839	1.6764	3.7238	0.128	3.2876	0.0463	0.5025	-0.2554	-0.3592	0.0061	-0.1069	0.3748	0.2438	-0.05	0.3766	0.0392	0.0552	0.2317	-0.0235	0.1703	34.1283	-15.5013	29.4354
5	3.8826	1.286	2.5349	4.3172	0.3076	3.117	0.1042	-0.0118	-0.0514	-0.1438	-0.012	0.2011	0.2162	-0.2271	-0.1017	0.1994	0.017	0.0514	0.1774	-0.0008	0.1484	25.486	-9.2196	39.8719
6	6.8029	0.8073	-5.5066	1.6762	-2.162	5.9406	-0.4741	0.2351	1.0102	-0.4539	0.4432	0.5563	-1.1091	-0.4931	-0.1223	0.503	0.0235	-0.2215	0.2745	0.0042	0.4008	16.933	5.6508	31.353
7	6.0304	-2.8795	-0.8622	4.5512	1.4362	2.3226	-0.0956	-0.0146	0.2345	-0.1894	-0.0583	0.6607	0.0575	-0.3108	0.0904	0.1786	-0.0277	-0.088	0.2114	0.0865	0.3908	-0.766	4.0434	-9.9259
8	4.8846	-2.0419	-1.6471	3.3499	1.3292	3.7998	-0.1302	-0.4763	0.2711	0.2938	0.2321	-0.0169	-0.0845	0.2019	-0.2073	0.1779	-0.0013	-0.0412	0.2876	0.0446	0.2023	12.7015	8.5277	-0.5468
9	5.22	0.4575	-2.2966	1.8248	-0.1072	3.1183	-0.0413	-0.159	0.161	-0.0908	0.049	0.299	0.0178	-0.0756	-0.0325	0.1455	0.0118	-0.0459	0.2049	0.046	0.2138	6.7728	6.5705	-8.3335
10	2.6426	0.3333	-0.528	3.9366	0.0285	4.9399	-0.0016	-0.4258	-0.5117	0.4252	0.1064	0.5336	0.679	-0.3579	-0.0383	0.3324	-0.0548	0.0139	0.2841	0.1061	0.3475	3.1571	-10.9345	0.9751
11	5.6056	2.5837	3.0952	4.0429	5.6526	8.1264	-0.0056	-0.2217	0.4453	0.6299	0.0352	-0.1528	0.0445	0.2665	-0.0597	0.258	0.0089	-0.0703	0.266	0.0183	0.2389	19.5833	6.9852	4.8515
12	0.6617	0.0106	1.7838	1.5984	0.064	5.0805	-0.1748	0.2237	0.369	0.0818	0.0591	0.4057	-0.2965	-0.0375	0.0988	0.2089	0.0457	-0.0035	0.2678	0.0114	0.277	16.5927	-0.5725	17.7519
13	0.8405	-0.3139	1.9628	2.0539	-0.2812	4.405	-0.2139	-0.0021	0.1433	0.1146	0.1785	-0.0753	-0.2944	-0.0858	-0.0061	0.2157	0.0002	0.0039	0.3109	0.0234	0.267	15.3253	-0.4198	15.6756

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 154 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 206 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 207 through 233 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 234 through 248 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 46 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 47 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 154 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 233 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 234 through 251 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 11 through 23 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 9 through 23 )

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