› 6dam

X-ray diffraction
1.85Å resolution

Crystal structure of lanthanide-dependent methanol dehydrogenase XoxF from Methylomicrobium buryatense 5G

Released:
DOI: 10.2210/pdb6dam/pdb
PDB entry 6dam coloured by chain, front view.
PDB entry 6dam coloured by chain, side view.
PDB entry 6dam coloured by chain, top view.
Source organism: Methylotuvimicrobium buryatense 5G
Primary publication:
Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C.
Deng YW, Ro SY, Rosenzweig AC
J Biol Inorg Chem 23 1037-1047 (2018)
PMID: 30132076

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104852 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lanthanide-dependent methanol dehydrogenase XoxF Chain: A
Molecule details ›
Chain: A
Length: 617 amino acids
Theoretical weight: 67.28 KDa
Source organism: Methylotuvimicrobium buryatense 5G
UniProt:
  • Canonical: A0A3F2YLY8 (Residues: 1-617; Coverage: 100%)
Sequence domains:
Structure domains: Quinoprotein alcohol dehydrogenase-like superfamily

Ligands and Environments

3 bound ligands:
Ligand LA 1 x LA
Ligand PQQ 1 x PQQ
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G, APS BEAMLINE 23-ID-B
Spacegroup: C2221
Unit cell:
a: 55.347Å b: 92.283Å c: 191.772Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.152 0.182

Quick links

Citations

7 review citations

The Chemistry of Lanthanides in Biology: Recent Discoveries, Emerging Principles, and Technological Applications.
Cotruvo JA. (2019)
6 more

2 mentions without citation

Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function.
Good et al. (2020)
1 more