9C3S

Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTATAC as recognition sequence

PDB DOI: https://doi.org/10.2210/pdb9C3S/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Burkholderia cenocepacia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-02 Released: 2024-09-11
Deposition Author(s): Kottur, J., Quintana-Feliciano, R., Aggarwal, A.K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.244
R-Value Work: 0.189
R-Value Observed: 0.192

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation

Quintana-Feliciano, R., Kottur, J., Ni, M., Ghosh, R., Salas-Estrada, L., Ahisen, G., Rechkobilt, O., Shapiro, L., Filizola, M., Fang, G., Aggarwal, A.K.

(2024) Nat Commun

Macromolecule Content

Total Structure Weight: 162.06 kDa
Atom Count: 10,295
Modelled Residue Count: 1,096
Deposited Residue Count: 1,244
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A, B, C, D	283	Burkholderia cenocepacia	Mutation(s): 0 Gene Names: JAO13_04290
UniProt
Find proteins for A0A8I1DKW0 (Burkholderia cepacia) Explore A0A8I1DKW0 Go to UniProtKB: A0A8I1DKW0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8I1DKW0
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA1	E, G, I, K	14	Burkholderia cenocepacia
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA2	F, H, J, L	14	Burkholderia cenocepacia
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	M	2		N/A	Interactions Focus chain M

Small Molecules

Ligands 1 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 N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D]	N [auth A], O [auth B], P [auth C], Q [auth D]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	M	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain M

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.244
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.728	α = 90
b = 137.728	β = 90
c = 167.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Quintana-Feliciano, R.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release

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 R01GM133198.