› 1yoe

X-ray diffraction
1.78Å resolution

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

Released:
DOI: 10.2210/pdb1yoe/pdb
PDB entry 1yoe coloured by chain, front view.
PDB entry 1yoe coloured by chain, side view.
PDB entry 1yoe coloured by chain, top view.
Source organism: Escherichia coli
Entry authors: Muzzolini L, Versees W, Steyaert J, Degano M

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154393 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrimidine-specific ribonucleoside hydrolase RihA Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 35.13 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P41409 (Residues: 2-311; Coverage: 100%)
Gene names: JW0646, b0651, rihA, ybeK
Sequence domains: Inosine-uridine preferring nucleoside hydrolase
Structure domains: Ribonucleoside hydrolase-like

Ligands and Environments

2 bound ligands:
Ligand RIB 1 x RIB
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: I222
Unit cell:
a: 76.466Å b: 84.062Å c: 112.483Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.167 0.193
Expression system: Escherichia coli

Quick links