5cms

X-ray diffraction
2.98Å resolution

Structural Insights into the Mechanism of Escherichia coli Ymdb

Released:

Function and Biology Details

Reaction catalysed:
2''-O-acetyl-ADP-D-ribose + H(2)O = ADP-D-ribose + acetate
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-141692 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-acetyl-ADP-ribose deacetylase Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Length: 183 amino acids
Theoretical weight: 19.64 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8D6 (Residues: 1-177; Coverage: 100%)
Gene names: JW1032, b1045, ymdB
Sequence domains: Macro domain
Structure domains: Leucine Aminopeptidase, subunit E, domain 1

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3121
Unit cell:
a: 290.019Å b: 290.019Å c: 114.324Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.222 0.25
Expression system: Escherichia coli