› 5a74

X-ray diffraction
2.5Å resolution

Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Mn

Released:
DOI: 10.2210/pdb5a74/pdb
PDB entry 5a74 coloured by chain, front view.
PDB entry 5a74 coloured by chain, side view.
PDB entry 5a74 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structure of the Homing Endonuclease I-CvuI Provides a New Template for Genome Modification.
Molina R, Redondo P, López-Méndez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G
J Biol Chem 290 28727-36 (2015)
PMID: 26363068

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118393 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA endonuclease I-CvuI Chains: A, B
Molecule details ›
Chains: A, B
Length: 172 amino acids
Theoretical weight: 19.29 KDa
Source organism: Chlorella vulgaris
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P56347 (Residues: 2-161; Coverage: 99%)
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: synthetic construct
Expression system: Not provided
10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 62.73Å b: 82.03Å c: 94.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.186 0.234
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 mentions without citation

Far-Reaching Dispersal of Borrelia burgdorferi Sensu Lato-Infected Blacklegged Ticks by Migratory Songbirds in Canada.
Scott et al. (2018)
1 more