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DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

X-ray diffraction
2.2Å resolution
PDB entry 1dio coloured by chain, front view.
PDB entry 1dio coloured by chain, side view.
PDB entry 1dio coloured by chain, top view.
Source organism: Klebsiella oxytoca
Assembly composition:
hetero hexamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexamer
Accessible surface area: 50741.55 Å2
Buried surface area: 31055.35 Å2
Dissociation area: 2,398.99 Å2
Dissociation energy (ΔGdiss): 22.12 kcal/mol
Dissociation entropy (TΔSdiss): 15.35 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-176799

Macromolecules

Diol/glycerol dehydratase large subunit domain-containing protein
Chains: A, L
Length: 554 amino acids
Theoretical weight: 60.41 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59470 (Residues: 1-554; Coverage: 100%)
Gene names: AI3012V1_3144, F6W21_13300, pddA, pduC
Pfam: Dehydratase large subunit
InterPro:
CATH: Diol/glycerol dehydratase, large subunit
SCOP: Diol dehydratase, alpha subunit
Diol/glycerol dehydratase large subunit domain-containing protein in PDB entry 1dio, assembly 1, front view.
Diol/glycerol dehydratase large subunit domain-containing protein in PDB entry 1dio, assembly 1, side view.
Diol/glycerol dehydratase large subunit domain-containing protein in PDB entry 1dio, assembly 1, top view.
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Diol dehydrase beta subunit
Chains: B, E
Length: 224 amino acids
Theoretical weight: 24.14 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59471 (Residues: 1-224; Coverage: 100%)
Gene name: pddB
Pfam: Dehydratase medium subunit
InterPro:
CATH: B12-dependent dehydatase associated subunit
SCOP: Diol dehydratase, beta subunit
Diol dehydrase beta subunit in PDB entry 1dio, assembly 1, front view.
Diol dehydrase beta subunit in PDB entry 1dio, assembly 1, side view.
Diol dehydrase beta subunit in PDB entry 1dio, assembly 1, top view.
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Diol dehydrase gamma subunit
Chains: G, M
Length: 173 amino acids
Theoretical weight: 19.2 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59472 (Residues: 1-173; Coverage: 100%)
Gene name: pddC
Pfam: Dehydratase small subunit
InterPro:
CATH: Propanediol/glycerol dehydratase, small subunit
SCOP: Diol dehydratase, gamma subunit
Diol dehydrase gamma subunit in PDB entry 1dio, assembly 1, front view.
Diol dehydrase gamma subunit in PDB entry 1dio, assembly 1, side view.
Diol dehydrase gamma subunit in PDB entry 1dio, assembly 1, top view.
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