› 6f9p

X-ray diffraction
2.4Å resolution

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

Released:
DOI: 10.2210/pdb6f9p/pdb
PDB entry 6f9p coloured by chain, front view.
PDB entry 6f9p coloured by chain, side view.
PDB entry 6f9p coloured by chain, top view.
Source organism: Flavobacterium sp. CF136
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. CF136
Expression system: Escherichia coli
UniProt:
  • Canonical: J3BZS6 (Residues: 1-372; Coverage: 100%)
Gene name: PMI10_03368

Ligands and Environments

4 bound ligands:
Ligand CL 4 x CL
Ligand RE 4 x RE
Ligand SO4 3 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 90.2Å b: 98.87Å c: 165.96Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.213
Expression system: Escherichia coli

Quick links

Citations

1 review citation

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

1 mention without citation

Trends in coordination of rhenium organometallic complexes in the Protein Data Bank.
Brink et al. (2022)