› 5i1t

X-ray diffraction
2.6Å resolution

2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Complex with Triacetylchitotriose

Released:
DOI: 10.2210/pdb5i1t/pdb
PDB entry 5i1t coloured by chain, front view.
PDB entry 5i1t coloured by chain, side view.
PDB entry 5i1t coloured by chain, top view.
Source organism: Clostridioides difficile 630
Primary publication:
Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.
Nocadello S, Minasov G, Shuvalova LS, Dubrovska I, Sabini E, Anderson WF
J Biol Chem 291 14915-26 (2016)
PMID: 27226615

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172742 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Sporulation stage II protein D amidase enhancer LytB N-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.45 KDa
Source organism: Clostridioides difficile 630
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q18CL6 (Residues: 28-354; Coverage: 92%)
Gene names: CD630_01240, spoIID
Sequence domains: Stage II sporulation protein

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand ZN 1 x ZN
Ligand NA 1 x NA
Ligand CL 1 x CL
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P3121
Unit cell:
a: 98.082Å b: 98.082Å c: 108.327Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.157 0.155 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Sporulation and Germination in Clostridial Pathogens.
Shen et al. (2019)
2 more

3 mentions without citation

Lytic transglycosylases: concinnity in concision of the bacterial cell wall.
Dik et al. (2017)
2 more