› 3khb

X-ray diffraction
2.9Å resolution

Crystal structure of Escherichia coli AlkB with Co(II) and 2-OG

Released:
DOI: 10.2210/pdb3khb/pdb
PDB entry 3khb coloured by chain, front view.
PDB entry 3khb coloured by chain, side view.
PDB entry 3khb coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
Holland PJ, Hollis T
PLoS One 5 e8680 (2010)
PMID: 20084272

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 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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 219 amino acids
Theoretical weight: 24.4 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 1-216; Coverage: 100%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand CO 2 x CO
Ligand AKG 2 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2
Unit cell:
a: 148.624Å b: 42.806Å c: 86.454Å
α: 90° β: 121.77° γ: 90°
R-values:
R R work R free
0.234 0.23 0.307
Expression system: Escherichia coli

Quick links

Citations

6 review citations

DNA repair by reversal of DNA damage.
Yi et al. (2013)
5 more

2 mentions without citation

Single-Molecule Analyte Recognition with ClyA Nanopores Equipped with Internal Protein Adaptors.
Soskine et al. (2015)
1 more