› 4d6o

X-ray diffraction
2.2Å resolution

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2)

Released:
DOI: 10.2210/pdb4d6o/pdb
PDB entry 4d6o coloured by chain, front view.
PDB entry 4d6o coloured by chain, side view.
PDB entry 4d6o coloured by chain, top view.
Source organisms:
Primary publication:
Visualizing phosphodiester-bond hydrolysis by an endonuclease.
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G
Nat Struct Mol Biol 22 65-72 (2015)
PMID: 25486305

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218958 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homing endonuclease I-DmoI Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 199 amino acids
Theoretical weight: 23.27 KDa
Source organism: Desulfurococcus mucosus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21505 (Residues: 2-188; Coverage: 96%)
Sequence domains: LAGLIDADG-like domain
Structure domains: Homing endonucleases
25MER Chains: B, H
Molecule details ›
Chains: B, H
Length: 25 nucleotides
Theoretical weight: 7.71 KDa
Source organism: synthetic construct
Expression system: Not provided
25MER Chains: C, I
Molecule details ›
Chains: C, I
Length: 25 nucleotides
Theoretical weight: 7.65 KDa
Source organism: synthetic construct
Expression system: Not provided
25MER Chain: E
Molecule details ›
Chain: E
Length: 25 nucleotides
Theoretical weight: 7.69 KDa
Source organism: synthetic construct
Expression system: Not provided
25MER Chain: F
Molecule details ›
Chain: F
Length: 25 nucleotides
Theoretical weight: 7.67 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 106.888Å b: 70.672Å c: 107.143Å
α: 90° β: 119.8° γ: 90°
R-values:
R R work R free
0.187 0.186 0.22
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing.
Stella et al. (2017)
1 more