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X-ray diffraction
1.8Å resolution

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83

Released:
DOI: 10.2210/pdb3bio/pdb
PDB entry 3bio coloured by chain, front view.
PDB entry 3bio coloured by chain, side view.
PDB entry 3bio coloured by chain, top view.
Source organism: Porphyromonas gingivalis W83
Entry authors: Nocek B, Mulligan R, Moy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reaction catalysed: 
Meso-2,6-diaminoheptanedioate + H(2)O + NADP(+) = L-2-amino-6-oxoheptanedioate + NH(3) + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-181764 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Meso-diaminopimelate D-dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 304 amino acids
Theoretical weight: 33.33 KDa
Source organism: Porphyromonas gingivalis W83
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7MW40 (Residues: 1-301; Coverage: 100%)
Gene name: PG_0806
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ACT 1 x ACT
Ligand EPE 2 x EPE
Ligand GOL 1 x GOL
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: R32
Unit cell:
a: 99.268Å b: 99.268Å c: 356.025Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.16 0.156 0.187
Expression system: Escherichia coli BL21(DE3)

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