› 2olo

X-ray diffraction
1.9Å resolution

NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: open form at 1.9A resolution

Released:
DOI: 10.2210/pdb2olo/pdb
PDB entry 2olo coloured by chain, front view.
PDB entry 2olo coloured by chain, side view.
PDB entry 2olo coloured by chain, top view.
Source organism: Streptomyces tendae
Primary publication:
NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution.
Carrell CJ, Bruckner RC, Venci D, Zhao G, Jorns MS, Mathews FS
Structure 15 928-41 (2007)
PMID: 17697998

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194968 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
FAD dependent oxidoreductase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 397 amino acids
Theoretical weight: 44.17 KDa
Source organism: Streptomyces tendae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9X9P9 (Residues: 1-389; Coverage: 100%)
Gene name: nikD
Sequence domains: FAD dependent oxidoreductase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand FAD 1 x FAD
Ligand 6PC 1 x 6PC
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: C2
Unit cell:
a: 87.71Å b: 90.57Å c: 85.4Å
α: 90° β: 118.54° γ: 90°
R-values:
R R work R free
0.184 0.184 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis.
Winn et al. (2010)
3 more

1 mention without citation

Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.
Kommoju et al. (2009)