› 4d6n

X-ray diffraction
2.35Å resolution

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MG (STATE 7)

Released:
DOI: 10.2210/pdb4d6n/pdb
PDB entry 4d6n coloured by chain, front view.
PDB entry 4d6n coloured by chain, side view.
PDB entry 4d6n 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 pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117303 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homing endonuclease I-DmoI Chains: A, F, K
Molecule details ›
Chains: A, F, K
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
5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3' Chains: B, G, L
Molecule details ›
Chains: B, G, L
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' Chains: C, H, M
Molecule details ›
Chains: C, H, M
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3' Chains: D, I, N
Molecule details ›
Chains: D, I, N
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' Chains: E, J, O
Molecule details ›
Chains: E, J, O
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand ACT 3 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 106.311Å b: 70.269Å c: 107.169Å
α: 90° β: 119.59° γ: 90°
R-values:
R R work R free
0.184 0.182 0.217
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