› 3dke

X-ray diffraction
1.25Å resolution

Polar and non-polar cavities in phage T4 lysozyme

Released:
DOI: 10.2210/pdb3dke/pdb
PDB entry 3dke coloured by chain, front view.
PDB entry 3dke coloured by chain, side view.
PDB entry 3dke coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme.
Liu L, Quillin ML, Matthews BW
Proc Natl Acad Sci U S A 105 14406-11 (2008)
PMID: 18780783

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133020 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endolysin Chain: X
Molecule details ›
Chain: X
Length: 164 amino acids
Theoretical weight: 18.76 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P00720 (Residues: 1-164; Coverage: 100%)
Gene name: E
Sequence domains: Phage lysozyme
Structure domains: Lysozyme

Ligands and Environments

7 bound ligands:
Ligand K 1 x K
Ligand CL 2 x CL
Ligand AZI 1 x AZI
Ligand EPE 1 x EPE
Ligand BME 2 x BME
Ligand HED 2 x HED
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P3221
Unit cell:
a: 60.226Å b: 60.226Å c: 96.677Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.156 0.155 0.173
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Lessons from the lysozyme of phage T4.
Baase et al. (2010)
13 other articles

6 mentions without citation

A review about nothing: are apolar cavities in proteins really empty?
Matthews et al. (2009)
5 more