› 2r0t

X-ray diffraction
1.9Å resolution

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine

Released:
DOI: 10.2210/pdb2r0t/pdb
PDB entry 2r0t coloured by chain, front view.
PDB entry 2r0t coloured by chain, side view.
PDB entry 2r0t coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation.
Cook PD, Holden HM
Biochemistry 46 14215-24 (2007)
PMID: 17997582

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: 44.34 KDa
Source organism: Escherichia coli
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

1 bound ligand:
Ligand PGU 2 x PGU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 69.908Å b: 72.905Å c: 86.959Å
α: 90° β: 107.94° γ: 90°
R-values:
R R work R free
0.185 0.183 0.255
Expression system: Escherichia coli

Quick links

Citations

4 review citations

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

3 mentions without citation

A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation.
Cook et al. (2007)
2 more