› 2fdj

X-ray diffraction
2.1Å resolution

Crystal Structure of AlkB in complex with Fe(II) and succinate

Released:
DOI: 10.2210/pdb2fdj/pdb
PDB entry 2fdj coloured by chain, front view.
PDB entry 2fdj coloured by chain, side view.
PDB entry 2fdj coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB.
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF
Nature 439 879-84 (2006)
PMID: 16482161

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138340 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 211 amino acids
Theoretical weight: 23.61 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand FE2 1 x FE2
Ligand SIN 1 x SIN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P1
Unit cell:
a: 36.769Å b: 38.705Å c: 40.261Å
α: 75.65° β: 74.65° γ: 66.23°
R-values:
R R work R free
0.178 0.178 0.229
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

33 review citations

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription.
Pastor et al. (2013)
32 more

6 mentions without citation

DynOmics: dynamics of structural proteome and beyond.
Li et al. (2017)
5 more