7QW5 | pdb_00007qw5

Adenine-specific DNA methyltransferase M.BseCI complexed with AdoHcy and cognate unmethylated DNA duplex

PDB DOI: https://doi.org/10.2210/pdb7QW5/pdb
NAKB: 7QW5

Classification: TRANSFERASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-24 Released: 2023-01-25
Deposition Author(s): Mitsikas, D.A., Kouyianou, K., Kotsifaki, D., Providaki, M., Bouriotis, V., Glykos, N.M., Kokkinidis, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.224 (Depositor), 0.225 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus.

Mitsikas, D.A., Kouyianou, K., Kotsifaki, D., Providaki, M., Bouriotis, V., Glykos, N.M., Kokkinidis, M.

To be published.

Macromolecule Content

Total Structure Weight: 74.24 kDa
Atom Count: 5,049
Modeled Residue Count: 564
Deposited Residue Count: 605
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase BseCI	A	585	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: bseCIM EC: 2.1.1.72
UniProt
Find proteins for P43423 (Geobacillus stearothermophilus) Explore P43423 Go to UniProtKB: P43423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43423
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
Unmethylated DNA duplex	B [auth Z]	10	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
Unmethylated DNA duplex	C [auth Y]	10	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.224 (Depositor), 0.225 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.04	α = 90
b = 87.04	β = 90
c = 156.35	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
CRANK	phasing
BUCCANEER	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	Greece	--

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection
Version 1.2: 2025-12-10
Changes: Data collection, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.