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Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA
 
 
DOI:10.2210/pdb3e54/pdb   NDB ID: PD1179
3E54
 
Primary Citation
spinning wheel
 
 
  •  
    Move Section Molecular Description Hide
    Classification: Hydrolase/dna
    Structure Weight: 52906.28
     
    Molecule:RRNA intron-encoded endonuclease
    Polymer:1Type:polypeptide(L)Length:169
    Chains:A, B
    EC#:3.1.-.- Go to IUBMB EC entry  
    Mutation:I65M, I107M
    Molecule:DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')
    Polymer:2Type:polydeoxyribonucleotideLength:13
    Chains:C
    Other Details:I-Vdi141I DNA Target Site
    Molecule:DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')
    Polymer:3Type:polydeoxyribonucleotideLength:9
    Chains:D
    Other Details:I-Vdi141I DNA Target Site
    Molecule:DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')
    Polymer:4Type:polydeoxyribonucleotideLength:13
    Chains:E
    Other Details:I-Vdi141I DNA Target Site
    Molecule:DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')
    Polymer:5Type:polydeoxyribonucleotideLength:9
    Chains:F
    Other Details:I-Vdi141I DNA Target Site
     
     
  •  
    Move Section Source Hide
    Polymer: 1
    Scientific Name: Vulcanisaeta distributa Go to NCBI Taxonomy entry Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
    Polymer: 3
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
    Polymer: 4
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
    Polymer: 5
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
     
     
  •  
    Move Section Ligand Chemical Component Hide
    Identifier Name Formula Interaction View Links
    EOH     ETHANOL C2 H6 O 3DLigand Explorer Link out to Ligand Expos:EOH Link out to SuperLigands:EOH Link out to SuperHapten:EOH
    MG     MAGNESIUM ION Mg 3DLigand Explorer Link out to Ligand Expos:MG Link out to SuperLigands:MG Link out to SuperHapten:MG
     
     
  •  
    Move Section Derived Data Hide
     
     
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< Biological Assembly 1    Help >
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Biological assembly 1 assigned by authors and generated by PISA (software)
 
 
 
  •  
    Move Section Deposition Summary Hide
    Authors:   Nomura, N.,   Nomura, Y.,   Sussman, D.,   Stoddard, B.L.

    Deposition:   2008-08-13
    Release:   2008-12-30
     
     
  •  
    Move Section Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Experimental Data:   Download Structure Factors
    View a histogram of Resolution Resolution[Å]: 2.50
    R-Value: 0.231 (obs.)
    R-Free: 0.250
    Space Group: P 61
    Unit Cell:
      Length [Å] Angles [°]
    a = 66.58 α = 90.00 
    b = 66.58 β = 90.00 
    c = 217.91 γ = 120.00