PDB-7dsu: Structure of Mod subunit of the Type III restriction-modification...

ID or keywords:

Entry

Database: PDB / ID: 7dsu

Title

Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V

Components

Mbo45V

Keywords

DNA BINDING PROTEIN / Methyltransferase / Type III restriction-modification enzyme / sinefungin / Beta-class of AdoMet-dependent methyltransferase

Function / homology

SINEFUNGIN

Function and homology information

Biological species

Mycoplasma bovis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.2 Å

Authors

Ahmed, I. / Chouhan, O.P. / Gopinath, A. / Morgan, R.D. / Bhagat, K. / Singh, A. / Saikrishnan, K.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V
Authors: Ahmed, I. / Chouhan, O.P. / Gopinath, A. / Morgan, R.D. / Bhagat, K. / Singh, A. / Saikrishnan, K.

History

Deposition	Jan 2, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 5, 2023	Group: Database references / Structure summary / Category: citation / entity / struct Item: _citation.title / _entity.pdbx_description / _struct.title
Revision 1.2	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7dsu.cif.gz	343.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7dsu.ent.gz	276.4 KB	Display	PDB format
PDBx/mmJSON format	7dsu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7dsu_validation.pdf.gz	929.1 KB	Display	wwPDB validaton report
Full document	7dsu_full_validation.pdf.gz	955.2 KB	Display
Data in XML	7dsu_validation.xml.gz	33.6 KB	Display
Data in CIF	7dsu_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/7dsu ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7dsu	HTTPS FTP

-
Related structure data

Similar structure data	6d56-d 6bvl-d 5wfq-d 1nvv-d 4nyj-d 6cuo-d 6p9o-d 6d5g-d 4e0j-1 6d5v-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: Mbo45V

B: Mbo45V

hetero molecules

134 kDa, 2 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)	95.296, 100.875, 187.316
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Mbo45V Mass: 66413.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma bovis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.42 Å³/Da / Density % sol: 64.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 3350, 0.1 M proline, 0.1 M Na-Hepes pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97887 Å
Detector	Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 30, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97887 Å / Relative weight: 1
Reflection	Resolution: 3.2→48.703 Å / Num. obs: 60724 / % possible obs: 99.5 % / Redundancy: 12.7 % / R_merge(I) obs: 0.132 / Net I/σ(I): 12.8
Reflection shell	Resolution: 3.2→3.37 Å / R_merge(I) obs: 1.102 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4374

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.2→48.703 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2853	2687	4.7 %
R_work	0.2261	-	-
obs	0.2288	57159	99.32 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→48.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6287	0	4	3	6294

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6398
X-RAY DIFFRACTION	f_angle_d	0.652	8710
X-RAY DIFFRACTION	f_dihedral_angle_d	15.237	3800
X-RAY DIFFRACTION	f_chiral_restr	0.044	1019
X-RAY DIFFRACTION	f_plane_restr	0.003	1132

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 (%)
3.2001-3.2582	0.3255	153	0.3096	2881	X-RAY DIFFRACTION	100
3.2582-3.3209	0.3196	171	0.283	2825	X-RAY DIFFRACTION	99
3.3209-3.3887	0.2778	145	0.2544	2895	X-RAY DIFFRACTION	99
3.3887-3.4623	0.2905	142	0.2569	2810	X-RAY DIFFRACTION	99
3.4623-3.5428	0.3069	168	0.2533	2851	X-RAY DIFFRACTION	99
3.5428-3.6314	0.2691	154	0.2598	2834	X-RAY DIFFRACTION	100
3.6314-3.7296	0.3038	174	0.2515	2843	X-RAY DIFFRACTION	99
3.7296-3.8393	0.316	167	0.2537	2830	X-RAY DIFFRACTION	99
3.8393-3.9631	0.3098	134	0.2433	2913	X-RAY DIFFRACTION	99
3.9631-4.1047	0.2913	124	0.2353	2846	X-RAY DIFFRACTION	100
4.1047-4.269	0.2521	139	0.2205	2861	X-RAY DIFFRACTION	99
4.269-4.4631	0.2829	97	0.1996	2940	X-RAY DIFFRACTION	99
4.4631-4.6983	0.2691	105	0.1921	2874	X-RAY DIFFRACTION	99
4.6983-4.9923	0.1895	118	0.19	2895	X-RAY DIFFRACTION	99
4.9923-5.3774	0.2553	138	0.2023	2874	X-RAY DIFFRACTION	99
5.3774-5.9177	0.2623	123	0.2252	2899	X-RAY DIFFRACTION	100
5.9177-6.772	0.301	152	0.2343	2870	X-RAY DIFFRACTION	100
6.772-8.5246	0.2323	117	0.2199	2896	X-RAY DIFFRACTION	100
8.5246-48.703	0.3386	166	0.2328	2835	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	-0.0136	0.0188	-0.0165	0.1793	0.047	0.0616	-0.4383	0.991	0.7585	-0.6119	0.5614	2.3888	-0.0628	-0.3629	-0.0408	1.8155	-0.4401	-0.1857	2.1448	-0.2176	2.2129	-37.9079	-9.515	-30.3164
2	2.5948	0.284	-0.9027	2.2655	0.4799	5.4184	-0.1396	-0.586	-0.1636	0.184	-0.0364	0.1765	0.5559	-0.5469	0.1368	0.7644	0.0166	0.1509	1.081	-0.0287	1.0546	-17.7197	13.5779	-3.8437
3	9.6819	-2.1548	-3.8714	5.005	1.9507	7.2401	-0.539	0.2896	-0.4018	0.879	0.9288	-0.4395	1.6544	0.9137	-0.0885	0.7785	0.1141	-0.1245	1.0449	-0.2163	1.0557	-1.1107	14.7121	-17.7284
4	0.1857	-0.6024	0.2339	5.7032	0.0959	4.3195	0.7151	0.4926	1.3799	-0.17	-0.1167	-0.1237	-1.8552	-0.2422	-0.1894	1.2312	0.1522	0.2369	1.0501	-0.0646	1.2207	-8.9506	35.0169	-18.3148
5	2.2688	2.152	-0.9455	2.1649	-0.5224	4.5863	-0.0243	-0.5641	0.2567	0.0619	0.0285	-0.1628	-0.1746	0.2687	0.0776	0.6996	0.0109	0.1091	1.0138	-0.2229	0.9727	-5.6809	25.4316	-4.6509
6	4.9272	4.3726	-1.4177	6.8089	-0.9175	3.9595	0.414	-0.9407	-0.2488	1.0866	-0.2551	-0.3887	-0.2558	0.7972	-0.1232	0.7829	0.1595	-0.0176	1.4741	-0.0808	0.8873	-6.553	21.0807	12.3763
7	2.3644	4.0185	1.9989	7.5353	1.2252	6.4405	0.0495	-1.1959	0.5113	0.3334	0.3181	1.2366	0.0774	-0.9426	-0.2355	1.092	-0.0382	0.2922	1.7412	0.1395	1.349	-28.602	15.7358	15.168
8	0.1188	-0.4469	-0.3374	1.6294	1.4971	2.0202	0.1276	-0.9527	-1.4149	-0.1532	0.445	0.9187	2.7814	0.272	0.7624	1.8117	-0.2562	0.0827	2.4309	0.2147	2.0937	-22.3177	-18.0629	-20.2177
9	4.8898	5.7028	5.0632	6.7319	5.9246	5.3168	0.2797	0.0761	-1.0029	-0.8177	-0.0238	-1.0834	0.6181	0.3471	0.1686	1.4369	-0.3513	0.0253	1.8315	-0.3361	1.5633	-23.4242	-8.5303	-26.26
10	3.3511	-0.392	0.3515	4.2689	1.9163	6.2976	-0.0395	0.2899	-0.1091	-0.7343	-0.2522	0.4636	0.1335	-0.7681	0.2951	0.9051	-0.0163	-0.0486	0.5917	-0.0426	0.8391	-11.2337	2.5197	-39.9869
11	1.1676	0.6136	-1.889	4.9142	1.4282	5.7279	0.0892	0.3066	0.2426	-0.9842	-0.1172	0.0229	-0.5477	-0.0406	0.0113	0.8612	0.0255	-0.0034	0.7039	-0.0205	0.8864	0.214	15.3677	-40.7393
12	4.7185	2.4781	-1.3806	3.291	0.5002	2.2493	-0.6682	0.945	-0.1084	-0.6529	0.6827	0.1486	-0.153	-0.0766	0.1832	1.4299	-0.0221	-0.1609	0.922	-0.1078	1.0253	-7.9332	-0.1883	-57.1121
13	2.3614	0.654	-0.1288	9.726	3.8058	4.6733	-0.0639	0.0438	-0.3911	-0.9576	-0.1329	-0.5596	0.1964	-0.4555	0.3634	1.2326	-0.0093	-0.2151	0.7984	0.0684	1.0772	-8.9115	-13.0365	-52.4732

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 212 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 213 through 236 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 237 through 363 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 364 through 456 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 457 through 511 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 512 through 552 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 35 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 36 through 62 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 63 through 212 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 213 through 481 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 482 through 525 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 526 through 548 )

-
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

-
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

-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

-
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