› 2vs8

X-ray diffraction
2.1Å resolution

The crystal structure of I-DmoI in complex with DNA and Mn

Released:
DOI: 10.2210/pdb2vs8/pdb
PDB entry 2vs8 coloured by chain, front view.
PDB entry 2vs8 coloured by chain, side view.
PDB entry 2vs8 coloured by chain, top view.
Source organism: Desulfurococcus mucosus
Primary publication:
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibés A, Serrano L, Grizot S, Duchateau P, Pâques F, Blanco FJ, Montoya G
Proc Natl Acad Sci U S A 105 16888-93 (2008)
PMID: 18974222

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-115882 (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: 200 amino acids
Theoretical weight: 23.4 KDa
Source organism: Desulfurococcus mucosus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21505 (Residues: 2-190; Coverage: 97%)
Sequence domains: LAGLIDADG-like domain
Structure domains: Homing endonucleases
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*A)-3' Chains: B, G, L
Molecule details ›
Chains: B, G, L
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
Source organism: Desulfurococcus mucosus
Expression system: Not provided
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP* DGP*DCP*DGP)-3' Chains: C, H, M
Molecule details ›
Chains: C, H, M
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Desulfurococcus mucosus
Expression system: Not provided
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*C)-3' Chains: D, I, N
Molecule details ›
Chains: D, I, N
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Desulfurococcus mucosus
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: Desulfurococcus mucosus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 107.134Å b: 70.634Å c: 106.955Å
α: 90° β: 119.85° γ: 90°
R-values:
R R work R free
0.203 0.201 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy.
Silva et al. (2011)
4 more

3 mentions without citation

Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
Marcaida et al. (2008)
2 more