› 3e54

X-ray diffraction
2.5Å resolution

Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA

Released:
DOI: 10.2210/pdb3e54/pdb
PDB entry 3e54 coloured by chain, front view.
PDB entry 3e54 coloured by chain, side view.
PDB entry 3e54 coloured by chain, top view.
Source organism: Vulcanisaeta distributa
Primary publication:
Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.
Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL
Nucleic Acids Res 36 6988-98 (2008)
PMID: 18984620

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116201 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homing endonuclease LAGLIDADG domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 169 amino acids
Theoretical weight: 19.62 KDa
Source organism: Vulcanisaeta distributa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6L703 (Residues: 1-169; Coverage: 100%)
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.9 KDa
Source organism: Vulcanisaeta distributa
Expression system: Not provided
DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3') Chain: D
Molecule details ›
Chain: D
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Vulcanisaeta distributa
Expression system: Not provided
DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3') Chain: E
Molecule details ›
Chain: E
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Vulcanisaeta distributa
Expression system: Not provided
DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3') Chain: F
Molecule details ›
Chain: F
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
Source organism: Vulcanisaeta distributa
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 5 x MG
Ligand EOH 3 x EOH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P61
Unit cell:
a: 66.58Å b: 66.58Å c: 217.91Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.231 0.231 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer.
Siva et al. (2021)
1 more

3 mentions without citation

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.
Nomura et al. (2008)
2 more