3bie

X-ray diffraction
1.68Å resolution

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

Released:

Function and Biology Details

Reaction catalysed:
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 202 amino acids
Theoretical weight: 22.44 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P05050 (Residues: 13-214; Coverage: 94%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.77 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-D
Spacegroup: P21
Unit cell:
a: 41.413Å b: 75.822Å c: 52.228Å
α: 90° β: 108.53° γ: 90°
R-values:
R R work R free
0.188 0.187 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided