› 7q4t

X-ray diffraction
1.27Å resolution

Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment.

Released:
DOI: 10.2210/pdb7q4t/pdb
PDB entry 7q4t coloured by chain, front view.
PDB entry 7q4t coloured by chain, side view.
PDB entry 7q4t coloured by chain, top view.
Source organisms:
Primary publication:
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain.
Vázquez R, Seoane-Blanco M, Rivero-Buceta V, Ruiz S, van Raaij MJ, García P
OpenAccess logo Acta Crystallogr D Struct Biol 78 435-454 (2022)
PMID: 35362467

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123530 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
N-acetylmuramidase domain-containing protein Chain: AAA
Molecule details ›
Chain: AAA
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Pseudomonas phage JG004
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F4YDQ3 (Residues: 1-186; Coverage: 100%)
Gene name: PJG4_087
Sequence domains: N-acetylmuramidase
ALA-DGL Chain: LbL
Molecule details ›
Chain: LbL
Length: 2 amino acids
Theoretical weight: 218 Da
Source organism: Pseudomonas aeruginosa PAO1

Ligands and Environments

Carbohydrate polymer : NEW Components: MUB, NAG
Carbohydrate polymer
2 bound ligands:
Ligand PEG 2 x PEG
Ligand EDO 13 x EDO
1 modified residue:
Ligand DGL 1 x DGL

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P212121
Unit cell:
a: 43.581Å b: 61.173Å c: 69.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.132 0.13 0.161
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Engineering strategies and challenges of endolysin as an antibacterial agent against Gram-negative bacteria.
Zheng et al. (2024)
1 more

2 mentions without citation

Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain.
Vázquez et al. (2022)
1 more