› 1y7m

X-ray diffraction
2.05Å resolution

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

Released:
DOI: 10.2210/pdb1y7m/pdb
PDB entry 1y7m coloured by chain, front view.
PDB entry 1y7m coloured by chain, side view.
PDB entry 1y7m coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS
Proteins 62 144-51 (2006)
PMID: 16287140

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128604 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative L,D-transpeptidase YkuD Chains: A, B
Molecule details ›
Chains: A, B
Length: 164 amino acids
Theoretical weight: 17.69 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O34816 (Residues: 1-164; Coverage: 100%)
Gene names: BSU14040, ykuD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand CD 2 x CD
Ligand SO4 4 x SO4
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P212121
Unit cell:
a: 56.276Å b: 63.91Å c: 93.679Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.211 0.27
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

LysM, a widely distributed protein motif for binding to (peptido)glycans.
Buist et al. (2008)
7 more

13 mentions without citation

Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view.
Visweswaran et al. (2011)
12 more