› 5k8c

X-ray diffraction
1.85Å resolution

X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis

Released:
DOI: 10.2210/pdb5k8c/pdb
PDB entry 5k8c coloured by chain, front view.
PDB entry 5k8c coloured by chain, side view.
PDB entry 5k8c coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Zachman-Brockmeyer TR, Thoden JB, Holden HM
Biochemistry 55 4485-94 (2016)
PMID: 27275764

Function and Biology Details

Reaction catalysed: 
3-deoxy-alpha-D-manno-octulopyranosonate + O(2) = 3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H(2)O(2)
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-184365 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-deoxy-alpha-D-manno-octulosonate 8-oxidase Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 39.67 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8EEB0 (Residues: 1-356; Coverage: 100%)
Gene names: SO_2477, kdnB
Sequence domains: Iron-containing alcohol dehydrogenase
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand NAD 1 x NAD
Ligand PO4 2 x PO4
Ligand CL 2 x CL
Ligand EDO 1 x EDO
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P6322
Unit cell:
a: 107.594Å b: 107.594Å c: 149.861Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.179 0.218
Expression system: Escherichia coli

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Citations

1 citations in other articles

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing.
Jaing et al. (2016)

1 mention without citation

Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Zachman-Brockmeyer et al. (2016)