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The crystal structure of I-LtrI

X-ray diffraction
2.704Å resolution
PDB entry 3r7p coloured by chain, front view.
PDB entry 3r7p coloured by chain, side view.
PDB entry 3r7p coloured by chain, top view.
Source organism: Leptographium truncatum
Assembly composition:
hetero pentamer (preferred)
Entry contents: 1 distinct polypeptide molecule
4 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Homing endonuclease LAGLIDADG domain-containing protein and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 19147.25 Å2
Buried surface area: 9720.76 Å2
Dissociation area: 2,007.74 Å2
Dissociation energy (ΔGdiss): 37.08 kcal/mol
Dissociation entropy (TΔSdiss): 11.95 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111771

Macromolecules

Homing endonuclease LAGLIDADG domain-containing protein
Chain: A
Length: 315 amino acids
Theoretical weight: 36.02 KDa
Source organism: Leptographium truncatum
Expression system: Escherichia coli
UniProt:
  • Canonical: C7SWF3 (Residues: 398-712; Coverage: 44%)
Gene names: HEG fusion, rps3
Pfam: LAGLIDADG endonuclease
InterPro:
CATH: Homing endonucleases
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 3r7p, assembly 1, front view.
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 3r7p, assembly 1, side view.
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 3r7p, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
Representative chains: B
Source organism: Leptographium truncatum [330483]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.91 KDa
DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3') in PDB entry 3r7p, assembly 1, front view.
DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3') in PDB entry 3r7p, assembly 1, side view.
DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3') in PDB entry 3r7p, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3')
Representative chains: C
Source organism: Leptographium truncatum [330483]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3') in PDB entry 3r7p, assembly 1, front view.
DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3') in PDB entry 3r7p, assembly 1, side view.
DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3') in PDB entry 3r7p, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)-3')
Representative chains: D
Source organism: Leptographium truncatum [330483]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.51 KDa
DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)-3') in PDB entry 3r7p, assembly 1, front view.
DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)-3') in PDB entry 3r7p, assembly 1, side view.
DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)-3') in PDB entry 3r7p, assembly 1, top view.
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DNA chain E
Name: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3')
Representative chains: E
Source organism: Leptographium truncatum [330483]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3') in PDB entry 3r7p, assembly 1, front view.
DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3') in PDB entry 3r7p, assembly 1, side view.
DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3') in PDB entry 3r7p, assembly 1, top view.
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