› 1ne8

X-ray diffraction
2.1Å resolution

YDCE protein from Bacillus subtilis

Released:
DOI: 10.2210/pdb1ne8/pdb
PDB entry 1ne8 coloured by chain, front view.
PDB entry 1ne8 coloured by chain, side view.
PDB entry 1ne8 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Crystal structure of YdcE protein from Bacillus subtilis.
Gogos A, Mu H, Bahna F, Gomez CA, Shapiro L
Proteins 53 320-2 (2003)
PMID: 14517982

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161232 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endoribonuclease EndoA Chain: A
Molecule details ›
Chain: A
Length: 117 amino acids
Theoretical weight: 13.06 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P96622 (Residues: 2-116; Coverage: 99%)
Gene names: BSU04660, mazF, ndoA, ydcE
Sequence domains: PemK-like, MazF-like toxin of type II toxin-antitoxin system
Structure domains: SH3 type barrels.

Ligands and Environments

2 bound ligands:
Ligand 1PG 2 x 1PG
Ligand ACY 2 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9A
Spacegroup: P6522
Unit cell:
a: 56.63Å b: 56.63Å c: 138.257Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.162 0.158 0.21
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

Toxin-antitoxin modules as bacterial metabolic stress managers.
Buts et al. (2005)
4 more

9 mentions without citation

Structural basis of mRNA recognition and cleavage by toxin MazF and its regulation by antitoxin MazE in Bacillus subtilis.
Simanshu et al. (2013)
8 more