› 6exf

X-ray diffraction
1.95Å resolution

Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/Lysine

Released:
DOI: 10.2210/pdb6exf/pdb
PDB entry 6exf coloured by chain, front view.
PDB entry 6exf coloured by chain, side view.
PDB entry 6exf coloured by chain, top view.
Source organism: Flavobacterium sp.
Primary publication:
Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
Bastard K, Isabet T, Stura EA, Legrand P, Zaparucha A
OpenAccess logo Sci Rep 8 16587 (2018)
PMID: 30410048

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125296 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-lysine 4-hydroxylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 372 amino acids
Theoretical weight: 41.82 KDa
Source organism: Flavobacterium sp.
Expression system: Escherichia coli
UniProt:
  • Canonical: J3BZS6 (Residues: 1-372; Coverage: 100%)
Gene name: PMI10_03368

Ligands and Environments

3 bound ligands:
Ligand FE 4 x FE
Ligand LYS 5 x LYS
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 91.721Å b: 99.618Å c: 165.819Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.213
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis.
Zwick et al. (2020)
1 more