› 2z1m

X-ray diffraction
2Å resolution

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

Released:
DOI: 10.2210/pdb2z1m/pdb
PDB entry 2z1m coloured by chain, front view.
PDB entry 2z1m coloured by chain, side view.
PDB entry 2z1m coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Entry authors: Niwa H, Kuramitsu S, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130460 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose 4,6-dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 345 amino acids
Theoretical weight: 39.39 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O67175 (Residues: 1-345; Coverage: 100%)
Gene names: aq_1082, gmd, rfbD
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains:

Ligands and Environments


Cofactor: Ligand NDP 2 x NDP
1 bound ligand:
Ligand GDP 2 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P21
Unit cell:
a: 58.799Å b: 151.164Å c: 85.934Å
α: 90° β: 108.6° γ: 90°
R-values:
R R work R free
0.2 0.198 0.233
Expression system: Escherichia coli

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