› 3c5m

X-ray diffraction
2.6Å resolution

Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199

Released:
DOI: 10.2210/pdb3c5m/pdb
PDB entry 3c5m coloured by chain, front view.
PDB entry 3c5m coloured by chain, side view.
PDB entry 3c5m coloured by chain, top view.
Source organism: Vibrio parahaemolyticus RIMD 2210633
Entry authors: Forouhar F, Abashidze M, Seetharaman J, Janjua H, Mao L, Xiao R, Owens LA, Wang D, Baran MC, Acton TB, Montelione GT, Hunt JF, Tong L, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183331 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oligogalacturonate lyase domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 396 amino acids
Theoretical weight: 45.69 KDa
Source organism: Vibrio parahaemolyticus RIMD 2210633
Expression system: Escherichia coli
UniProt:
  • Canonical: Q87K10 (Residues: 1-388; Coverage: 100%)
Gene name: VPA0088
Sequence domains: Oligogalacturonate lyase
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase

Ligands and Environments

1 bound ligand:
Ligand MN 3 x MN
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P321
Unit cell:
a: 115.233Å b: 115.233Å c: 209.95Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.234 0.277
Expression system: Escherichia coli

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