› 5akn

X-ray diffraction
2.75Å resolution

THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN

Released:
DOI: 10.2210/pdb5akn/pdb
PDB entry 5akn coloured by chain, front view.
PDB entry 5akn coloured by chain, side view.
PDB entry 5akn coloured by chain, top view.
Source organisms:
Primary publication:
Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.
Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J
J Biol Chem 290 18534-44 (2015)
PMID: 26045557

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-118399 (preferred)
Entry contents:
1 distinct polypeptide molecule
6 distinct DNA molecules
Macromolecules (7 distinct):
Homing endonuclease I-DmoI Chains: A, F, K
Molecule details ›
Chains: A, F, K
Length: 199 amino acids
Theoretical weight: 23.21 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(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' Chains: B, G
Molecule details ›
Chains: B, G
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3 Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*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
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' Chains: H, M
Molecule details ›
Chains: H, M
Length: 26 nucleotides
Theoretical weight: 7.97 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3' Chain: L
Molecule details ›
Chain: L
Length: 29 nucleotides
Theoretical weight: 8.9 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 6 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 107.1Å b: 70.34Å c: 107.17Å
α: 90° β: 119.81° γ: 90°
R-values:
R R work R free
0.178 0.175 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Nick-initiated homologous recombination: Protecting the genome, one strand at a time.
Vriend et al. (2017)
1 more

1 mention without citation

Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.
Molina et al. (2015)