› 6dnw

X-ray diffraction
2.85Å resolution

Sequence Requirements of the Listeria innocua prophage attP site

Released:
DOI: 10.2210/pdb6dnw/pdb
PDB entry 6dnw coloured by chain, front view.
PDB entry 6dnw coloured by chain, side view.
PDB entry 6dnw coloured by chain, top view.
Source organism: Listeria innocua Clip11262
Primary publication:
Serine Integrase attP Binding and Specificity.
Li H, Sharp R, Rutherford K, Gupta K, Van Duyne GD
J Mol Biol 430 4401-4418 (2018)
PMID: 30227134

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119747 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Integrase [Bacteriophage A118] Chain: A
Molecule details ›
Chain: A
Length: 319 amino acids
Theoretical weight: 37.93 KDa
Source organism: Listeria innocua Clip11262
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q928V6 (Residues: 134-452; Coverage: 71%)
Gene name: int
Sequence domains:
DNA (26-MER) Chain: B
Molecule details ›
Chain: B
Length: 26 nucleotides
Theoretical weight: 7.91 KDa
Source organism: Listeria innocua Clip11262
Expression system: Not provided
DNA (26-MER) Chain: C
Molecule details ›
Chain: C
Length: 26 nucleotides
Theoretical weight: 8.07 KDa
Source organism: Listeria innocua Clip11262
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 48.291Å b: 57.112Å c: 167.883Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.219 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 citation in other articles

High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.
Bessen et al. (2019)
6 more

1 mention without citation

Serine Integrase attP Binding and Specificity.
Li et al. (2018)