› 1cw0

X-ray diffraction
2.3Å resolution

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA

Released:
DOI: 10.2210/pdb1cw0/pdb
PDB entry 1cw0 coloured by chain, front view.
PDB entry 1cw0 coloured by chain, side view.
PDB entry 1cw0 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
Tsutakawa SE, Jingami H, Morikawa K
Cell 99 615-23 (1999)
PMID: 10612397

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113561 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA mismatch endonuclease Vsr Chain: A
Molecule details ›
Chain: A
Length: 155 amino acids
Theoretical weight: 17.91 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P09184 (Residues: 2-156; Coverage: 99%)
Gene names: JW1943, b1960, vsr
Sequence domains: DNA mismatch endonuclease Vsr
Structure domains: VSR Endonuclease
DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3') Chain: M
Molecule details ›
Chain: M
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*AP*GP*C)-3') Chain: N
Molecule details ›
Chain: N
Length: 3 nucleotides
Theoretical weight: 887 Da
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3') Chain: O
Molecule details ›
Chain: O
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL24XU
Spacegroup: P65
Unit cell:
a: 63Å b: 63Å c: 152.5Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.204 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Structure and function of type II restriction endonucleases.
Pingoud et al. (2001)
14 more

12 mentions without citation

Short Peptides for Hydrolase Supramolecular Mimicry and Their Potential Applications.
Alletto et al. (2023)
11 more