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), 0.231 (DCC)
R-Value Observed:
0.229 (Depositor)

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.231 (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

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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

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