4GON

Crystal Structure of E. coli DNA Adenine Methyltransferase in Complex with Indole Aza-SAM

PDB DOI: https://doi.org/10.2210/pdb4GON/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-20 Released: 2014-02-26
Deposition Author(s): Harmer, J.E., Roach, P.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.258
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Basis of Selective N-6 adenine methyltransferase Inhibition by Transition State Mimic

Harmer, J.E., McKelvie, J.C., Hobley, G., Roach, P.L.

To be published.

Macromolecule Content

Total Structure Weight: 97.96 kDa
Atom Count: 6,180
Modelled Residue Count: 731
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA adenine methylase	A [auth D], B [auth E], C [auth F]	278	Escherichia coli K-12	Mutation(s): 0 Gene Names: b3387, dam, JW3350 EC: 2.1.1.72
UniProt
Find proteins for P0AEE8 (Escherichia coli (strain K12)) Explore P0AEE8 Go to UniProtKB: P0AEE8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0Y1 Query on 0Y1 Download Ideal Coordinates CCD File SDF format, chain D SDF format, chain E SDF format, chain F MOL2 format, chain D MOL2 format, chain E MOL2 format, chain F	D, E, F	5'-{[(3S)-3-amino-3-carboxypropyl][2-(1H-indol-3-yl)ethyl]amino}-5'-deoxyadenosine C₂₄ H₃₀ N₈ O₅ OIXWDGFFHFFLEE-WUASKDLJSA-N		Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.258
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.315	α = 90
b = 161.315	β = 90
c = 95.134	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-26
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.