› 1xm5

X-ray diffraction
2.7Å resolution

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

Released:
DOI: 10.2210/pdb1xm5/pdb
PDB entry 1xm5 coloured by chain, front view.
PDB entry 1xm5 coloured by chain, side view.
PDB entry 1xm5 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The ybeY protein from Escherichia coli is a metalloprotein.
Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA
Acta Crystallogr Sect F Struct Biol Cryst Commun 61 959-63 (2005)
PMID: 16511207

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141688 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endoribonuclease YbeY Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 155 amino acids
Theoretical weight: 17.54 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A898 (Residues: 1-155; Coverage: 100%)
Gene names: JW0656, b0659, ybeY
Sequence domains: Endoribonuclease YbeY
Structure domains: Metalloproteases ("zincins"), catalytic domain

Ligands and Environments

1 bound ligand:
Ligand NI 4 x NI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 46.073Å b: 119.613Å c: 132.903Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.234 0.273
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
Manjasetty et al. (2008)
2 more

9 mentions without citation

A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq.
Pandey et al. (2011)
8 more