PDB-4mb7: Crystal Structure of a viral DNA glycosylase

ID or keywords:

Entry

Database: PDB / ID: 4mb7

Title

Crystal Structure of a viral DNA glycosylase

Components

Endonuclease 8-like L720

Keywords

HYDROLASE /

zinc-finger domain / H2TH-motif /

DNA Glycosylase

Function / homology

Function and homology information

hydrolase activity, hydrolyzing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function

Biological species

Acanthamoeba polyphaga mimivirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.04 Å

Authors

Prakash, A. / Eckenroth, B.E. / Doublie, S.

Citation

Journal: Dna Repair / Year: 2013
Title: Structural investigation of a viral ortholog of human NEIL2/3 DNA glycosylases.
Authors: Prakash, A. / Eckenroth, B.E. / Averill, A.M. / Imamura, K. / Wallace, S.S. / Doublie, S.

History

Deposition	Aug 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2013	Group: Database references
Revision 1.2	Feb 28, 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 / struct_site 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mb7.cif.gz	131 KB	Display	PDBx/mmCIF format
PDB format	pdb4mb7.ent.gz	103.1 KB	Display	PDB format
PDBx/mmJSON format	4mb7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mb/4mb7 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mb7	HTTPS FTP

-
Related structure data

Similar structure data	3q13-d 6j9h-1 1wdv-d 1f46-d 6njq-2 6uep-1 4rwj-2 5t8q-2 1tnd-3 1sdj-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Endonuclease 8-like L720

hetero molecules

32.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Endonuclease 8-like L720

hetero molecules

A: Endonuclease 8-like L720

hetero molecules

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

Unit cell

Length a, b, c (Å)	121.670, 121.670, 164.180
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-509- HOH
2	1	A-510- HOH
3	1	A-519- HOH
4	1	A-534- HOH

#1: Protein	Endonuclease 8-like L720 / Endonuclease VIII-like L720 Mass: 32318.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: Endonuclease VIII (nei) 2, MIMI_L720 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) Plys S References: UniProt: Q5UNW7, DNA-(apurinic or apyrimidinic site) lyase, DNA-formamidopyrimidine glycosylase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.62 Å³/Da / Density % sol: 66 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6.8 Details: 20% (w/v) polyethylene glycol 3350, and 0.2 M sodium sulfate decahydrate , pH 6.8, VAPOR DIFFUSION, temperature 291K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9173 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9173 Å / Relative weight: 1

Reflection

Redundancy: 12.3 % / Number: 268736 / R_merge(I) obs: 0.147 / Χ²: 1.05 / D res high: 2.25 Å / D res low: 14 Å / Num. obs: 21805 / % possible obs: 99.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.79	14	100	1	0.076	1.025	13.5
3.83	4.79	100	1	0.078	1.057	13.9
3.35	3.83	100	1	0.106	1.055	13.8
3.05	3.35	100	1	0.156	1.076	13.8
2.83	3.05	100	1	0.251	1.082	13.8
2.67	2.83	100	1	0.361	1.082	13.7
2.53	2.67	100	1	0.441	1.071	13.4
2.42	2.53	100	1	0.513	1.054	11.9
2.33	2.42	99.8	1	0.576	1.012	8.9
2.25	2.33	95.3	1	0.636	0.954	6

Reflection

Resolution: 2.04→64.76 Å / Num. all: 29962 / Redundancy: 10.1 % / B_iso Wilson estimate: 27.64 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 9.5

Reflection shell

Resolution: 2.04→2.09 Å / Redundancy: 10.5 % / R_merge(I) obs: 0.665 / Mean I/σ(I) obs: 3.3

-
Phasing

Phasing	Method: SIRAS
Phasing dm	FOM : 0.8 / FOM acentric: 0.8 / FOM centric: 0.78 / Reflection: 7445 / Reflection acentric: 6726 / Reflection centric: 719
Phasing dm shell	Resolution: 3.2→3.4 Å / FOM : 0.7 / FOM acentric: 0.7 / FOM centric: 0.68 / Reflection: 1306 / Reflection acentric: 1215 / Reflection centric: 91

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
SOLVE	2.15	phasing
RESOLVE	2.15	phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

SIRAS / Resolution: 2.04→38.703 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2253	3043	10.16 %
R_work	0.1854	-	-
obs	0.1895	29953	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.365 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→38.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2203	0	16	182	2401

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2317
X-RAY DIFFRACTION	f_angle_d	0.916	3145
X-RAY DIFFRACTION	f_dihedral_angle_d	11.264	876
X-RAY DIFFRACTION	f_chiral_restr	0.056	351
X-RAY DIFFRACTION	f_plane_restr	0.004	390

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 (%)
2.04-2.0719	0.284	159	0.235	1210	X-RAY DIFFRACTION	100
2.0719-2.1059	0.3088	126	0.2182	1210	X-RAY DIFFRACTION	100
2.1059-2.1422	0.2388	127	0.1981	1204	X-RAY DIFFRACTION	100
2.1422-2.1812	0.2538	155	0.1887	1199	X-RAY DIFFRACTION	100
2.1812-2.2231	0.234	138	0.192	1218	X-RAY DIFFRACTION	100
2.2231-2.2685	0.2468	136	0.201	1192	X-RAY DIFFRACTION	100
2.2685-2.3178	0.2225	145	0.191	1221	X-RAY DIFFRACTION	100
2.3178-2.3717	0.2267	125	0.1894	1211	X-RAY DIFFRACTION	100
2.3717-2.431	0.2413	136	0.1957	1209	X-RAY DIFFRACTION	100
2.431-2.4967	0.2424	147	0.1864	1202	X-RAY DIFFRACTION	100
2.4967-2.5702	0.235	125	0.1821	1227	X-RAY DIFFRACTION	100
2.5702-2.6531	0.2206	127	0.1855	1250	X-RAY DIFFRACTION	100
2.6531-2.7479	0.2328	135	0.2006	1198	X-RAY DIFFRACTION	100
2.7479-2.8579	0.2785	137	0.2096	1214	X-RAY DIFFRACTION	100
2.8579-2.9879	0.2602	137	0.2037	1239	X-RAY DIFFRACTION	100
2.9879-3.1454	0.227	151	0.1915	1208	X-RAY DIFFRACTION	100
3.1454-3.3424	0.1998	139	0.1885	1230	X-RAY DIFFRACTION	100
3.3424-3.6003	0.2026	135	0.1728	1230	X-RAY DIFFRACTION	100
3.6003-3.9622	0.2137	139	0.168	1235	X-RAY DIFFRACTION	100
3.9622-4.5348	0.1586	136	0.1542	1246	X-RAY DIFFRACTION	100
4.5348-5.7105	0.199	141	0.159	1248	X-RAY DIFFRACTION	100
5.7105-38.7104	0.2723	147	0.2138	1309	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	0.0184	-0.0007	0.0131	0.0015	0.0004	0.0105	0.1108	-0.0629	-0.1123	0.0013	0.0787	-0.0747	0.0592	0.0293	0	0.2106	0.0471	0.0012	0.1756	0.0075	0.2197	18.3919	47.0795	60.8241
2	0.027	0.0188	0.0377	0.1879	0.1329	0.1131	-0.061	0.047	0.2267	-0.2451	-0.0437	0.056	-0.0075	-0.0078	-0.0279	0.19	0.0275	0.04	0.192	0.023	0.2213	9.648	60.3651	48.3611
3	0.0419	-0.0302	0.0228	0.0466	0.0349	0.037	-0.0329	0.0367	0.0568	-0.0383	0.0306	-0.0699	0.0132	-0.0652	-0	0.1736	-0	0.0246	0.1379	0.021	0.1791	14.7348	60.1573	58.3041
4	0.0023	-0.0016	-0.006	0.0038	0.0056	0.0041	-0.052	0.0876	-0.1524	-0.0279	0.1458	0.2576	0.1923	-0.1455	0	0.286	-0.0245	0.0654	0.2467	-0.0162	0.2398	6.3614	45.2948	53.2172
5	0.0796	0.0199	0.0226	0.0339	0.0158	0.0095	-0.0643	0.1362	0.0932	-0.1607	0.092	0.0342	0.0252	-0.0486	0.0109	0.2167	-0.0269	0.0669	0.1935	-0.0374	0.2038	9.9294	52.7871	51.2608
6	0.0232	-0.0167	-0.0041	0.0131	0.0081	0.006	0.0224	-0.0435	0.0165	0.0674	-0.0137	-0.1976	0.0195	0.0844	-0	0.1994	0.006	0.0267	0.1858	-0.0097	0.2511	7.0633	66.4028	68.336
7	0.0013	0.005	0.0034	0.0121	0.0114	0.0088	-0.0183	-0.0687	0.0962	0.0082	0.0291	0.0266	-0.0121	0.0811	-0	0.2195	0.0461	-0.01	0.1884	-0.013	0.2101	15.0191	63.7788	70.8345
8	0.0041	0.008	0	0.0139	-0.0035	0.0127	-0.1241	-0.1299	-0.0877	0.1703	0.1207	-0.106	-0.1701	0.0323	-0.0001	0.2894	0.0788	-0.0328	0.2573	0.0105	0.2413	20.6886	53.9595	80.8644
9	0.0097	0.0173	-0.0076	0.0394	0.0092	0.0244	-0.0595	-0.201	-0.0127	-0.0348	0.227	0.065	-0.1748	-0.1972	0.074	0.2135	0.1211	0.0446	0.3785	0.0781	0.2053	9.0452	51.0924	82.1809
10	0.218	0.2634	0.2071	0.3443	0.2713	0.2268	0.0646	-0.1006	-0.2325	-0.0174	0.3957	0.0566	-0.0093	-0.2805	0.2933	0.2211	-0.0187	-0.0162	0.4476	0.1985	0.2572	9.9092	41.0226	86.6089
11	0.806	0.1136	-0.1786	0.0437	-0.015	0.1279	0.1646	-0.2518	-0.0559	-0.0928	0.0396	0.0119	0.0978	0.0707	0.059	0.2653	0.0523	-0.0562	0.1743	0.0159	0.2211	20.3859	39.5992	74.9934
12	0.111	-0.1223	0.0983	0.1859	-0.1154	0.2179	0.292	-0.2159	-0.2658	-0.0975	0.2614	0.1161	0.3586	-0.3519	0.8198	0.3028	-0.2549	-0.3864	0.5139	0.2426	0.3873	8.5917	30.1941	77.5327
13	0.0065	-0.0036	0.007	0.004	-0.0067	0.0183	0.0635	-0.0172	0.0553	0.0389	-0.0209	0.0752	0.0502	-0.1685	-0.016	0.1792	-0.0504	-0.1685	0.6971	0.4088	0.4375	2.9576	39.6971	83.5844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 40 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 70 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 89 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 90 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 123 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 124 through 140 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 141 through 162 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 163 through 182 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 183 through 205 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 206 through 232 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 233 through 259 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 260 through 274 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi