4GON | pdb_00004gon

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor), 0.203 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4GON

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
Modeled Residue Count: 731
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 F SDF format, chain E SDF format, chain D MOL2 format, chain F MOL2 format, chain E MOL2 format, chain D mmCIF format, chain F mmCIF format, chain E mmCIF format, chain D	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 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor), 0.203 (DCC)
R-Value Observed: 0.212 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.