› 3b8x

X-ray diffraction
1.7Å resolution

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine

Released:
DOI: 10.2210/pdb3b8x/pdb
PDB entry 3b8x coloured by chain, front view.
PDB entry 3b8x coloured by chain, side view.
PDB entry 3b8x coloured by chain, top view.
Source organism: Escherichia coli O55:H7
Primary publication:
GDP-4-keto-6-deoxy-D-mannose 3-dehydratase, accommodating a sugar substrate in the active site.
Cook PD, Holden HM
J Biol Chem 283 4295-303 (2008)
PMID: 18045869

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190234 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
WbdK Chains: A, B
Molecule details ›
Chains: A, B
Length: 390 amino acids
Theoretical weight: 44.33 KDa
Source organism: Escherichia coli O55:H7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9F118 (Residues: 1-388; Coverage: 100%)
Gene names: NCTC8959_01918, wbdK
Sequence domains: DegT/DnrJ/EryC1/StrS aminotransferase family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NA 8 x NA
Ligand G4M 2 x G4M
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 62.411Å b: 98.123Å c: 119.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.173 0.26
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The structural biology of enzymes involved in natural product glycosylation.
Singh et al. (2012)
2 more

2 mentions without citation

Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential.
Vogel et al. (2022)
1 more