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

X-ray diffraction
2.4Å resolution
PDB entry 4ut0 coloured by chain, front view.
PDB entry 4ut0 coloured by chain, side view.
PDB entry 4ut0 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 1 distinct polypeptide molecule
4 distinct DNA molecules

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Assemblies

Assembly 1
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Assembly Name: Homing endonuclease I-DmoI and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 14010.0 Å2
Buried surface area: 8166.83 Å2
Dissociation area: 1,435.22 Å2
Dissociation energy (ΔGdiss): 18.75 kcal/mol
Dissociation entropy (TΔSdiss): 11.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118214
Assembly 2 (preferred)
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Assembly Name: Homing endonuclease I-DmoI and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 14245.59 Å2
Buried surface area: 8542.18 Å2
Dissociation area: 1,194.94 Å2
Dissociation energy (ΔGdiss): 26.55 kcal/mol
Dissociation entropy (TΔSdiss): 10.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118214
Assembly 3
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Assembly Name: Homing endonuclease I-DmoI and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 14352.65 Å2
Buried surface area: 8481.07 Å2
Dissociation area: 1,432.54 Å2
Dissociation energy (ΔGdiss): 17.84 kcal/mol
Dissociation entropy (TΔSdiss): 11.29 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118214

Macromolecules

Homing endonuclease I-DmoI
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%)
Pfam: LAGLIDADG-like domain
InterPro:
CATH: Homing endonucleases
Homing endonuclease I-DmoI in PDB entry 4ut0, assembly 2, front view.
Homing endonuclease I-DmoI in PDB entry 4ut0, assembly 2, side view.
Homing endonuclease I-DmoI in PDB entry 4ut0, assembly 2, top view.
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DNA chains B, G, L
Name: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
Representative chains: B, G, L
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' in PDB entry 4ut0, assembly 2, front view.
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' in PDB entry 4ut0, assembly 2, side view.
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' in PDB entry 4ut0, assembly 2, top view.
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DNA chains C, H, M
Name: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
Representative chains: C, H, M
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' in PDB entry 4ut0, assembly 2, front view.
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' in PDB entry 4ut0, assembly 2, side view.
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' in PDB entry 4ut0, assembly 2, top view.
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DNA chains D, I, N
Name: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
Representative chains: D, I, N
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' in PDB entry 4ut0, assembly 2, front view.
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' in PDB entry 4ut0, assembly 2, side view.
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' in PDB entry 4ut0, assembly 2, top view.
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DNA chains E, J, O
Name: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
Representative chains: E, J, O
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' in PDB entry 4ut0, assembly 2, front view.
5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' in PDB entry 4ut0, assembly 2, side view.
5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' in PDB entry 4ut0, assembly 2, top view.
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