› 5epd

X-ray diffraction
2.1Å resolution

Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)

Released:
DOI: 10.2210/pdb5epd/pdb
PDB entry 5epd coloured by chain, front view.
PDB entry 5epd coloured by chain, side view.
PDB entry 5epd coloured by chain, top view.
Source organism: Agrobacterium tumefaciens
Primary publication:
The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.
Zahradník J, Kolenko P, Palyzová A, Černý J, Kolářová L, Kyslíková E, Marešová H, Grulich M, Nunvar J, Šulc M, Kyslík P, Schneider B
PLoS One 13 e0195299 (2018)
PMID: 29630677

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100795 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 385 amino acids
Theoretical weight: 41.14 KDa
Source organism: Agrobacterium tumefaciens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0A0VDJ9 (Residues: 1-365; Coverage: 100%)
Gene name: xdpB
Sequence domains: NADH:flavin oxidoreductase / NADH oxidase family
Structure domains: Aldolase class I

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P212121
Unit cell:
a: 54.885Å b: 68.599Å c: 93.677Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.262
Expression system: Escherichia coli BL21(DE3)

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Citations

1 mention without citation

The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.
Zahradník et al. (2018)