7DSU | pdb_00007dsu

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

PDB DOI: https://doi.org/10.2210/pdb7DSU/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycoplasmopsis bovis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-02 Released: 2022-01-05
Deposition Author(s): Ahmed, I., Chouhan, O.P., Gopinath, A., Morgan, R.D., Bhagat, K., Singh, A., Saikrishnan, K.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.285 (Depositor), 0.290 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 133.65 kDa
Atom Count: 6,294
Modeled Residue Count: 832
Deposited Residue Count: 1,134
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mbo45V	A, B	567	Mycoplasmopsis bovis	Mutation(s): 0
UniProt
Find proteins for A0A2N8U1P8 (Mycoplasmopsis bovis) Explore A0A2N8U1P8 Go to UniProtKB: A0A2N8U1P8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2N8U1P8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG (Subject of Investigation/LOI) Query on SFG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.285 (Depositor), 0.290 (DCC)
R-Value Work: 0.226 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.296	α = 90
b = 100.875	β = 90
c = 187.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-05

Deposition Author(s):

Saikrishnan, K.

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--

Revision History (Full details and data files)

Version 1.0: 2022-01-05
Type: Initial release
Version 1.1: 2023-04-05
Changes: Database references, Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.