3BIE

X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 3BIE

Classification: Oxidoreductase / DNA

Total Structure Weight: 30356.90


Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-ketoglutarate-dependent dioxygenase alkB A 202 Escherichia coli EC#: 1.14.11.33 IUBMB
Fragment: catalytic domain
Mutation: S129C
Gene Name(s): alkB aidD b2212 JW2200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3') B 12 synthetic
DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3') C 13 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AKG
Query on AKG

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MA7
Query on MA7
B DNA LINKING C11 H17 N5 O6 P DA
2YR
Query on 2YR
B NON-POLYMER C11 H18 N3 O7 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.187
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.41 α = 90.00
b = 75.82 β = 108.53
c = 52.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-30
  • Released Date: 2008-04-22
  • Deposition author(s): Yi, C., Yang, C.-G.

Revision History

  • Version 1_0: 2008-04-22

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance

  • Version 1_2: 2014-05-28

    Type: Non-polymer description, Structure summary