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Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
 
 
DOI:10.2210/pdb2dy4/pdb   NDB ID: PD0864
2DY4
 
Primary Citation
spinning wheel
 
 
  •  
    Move Section Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 463958.64
     
    Molecule:5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
    Polymer:1Type:polydeoxyribonucleotideLength:18
    Chains:E, G, I, K
    Molecule:5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
    Polymer:2Type:polydeoxyribonucleotideLength:15
    Chains:F, H, J, L
    Molecule:DNA polymerase
    Polymer:3Type:polypeptide(L)Length:903
    Chains:A, B, C, D
    EC#:2.7.7.7 Go to IUBMB EC entry  
    Mutation:D222A, D327A
     
     
  •  
    Move Section Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
    Polymer: 2
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
    Polymer: 3
    Scientific Name: Enterobacteria phage rb69 Go to NCBI Taxonomy entry Expression System: Escherichia coli bl21(de3)  
     
     
  •  
    Move Section Related PDB Entries Hide
    Id Details
    1CLQ  RB69 GP43 complexed with undamaged DNA in exonuclease active site 
    1IG9  RB69 GP43 complexed with undamaged DNA in exonuclease active site 
    1Q9X  RB69 GP43 complexed with tetrahydrofuran containing DNA 
    1Q9Y  RB69 GP43 complexed with 8-oxoguanosine containing DNA 
    1RV2  RB69 GP43 complexed with DNA containing an abasic site analog 
    2DTU  Beta hairpin loop deletion variant of RB69 GP43 complexed with DNA containing an abasic site analog 
     
     
  •  
    Move Section Modified Residues Hide
    Identifier Name Formula Interaction View Links
    CTG (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE (parent: DT)(type: dnaLinking) C10 H17 N2 O10 P 3D Ligand Explorer Link out to Ligand Expos:CTG Link out to SuperLigands:CTG Link out to SuperHapten:CTG 2D
    MSE SELENOMETHIONINE (parent: MET)(type: lPeptideLinking) C5 H11 N O2 Se 3D Ligand Explorer Link out to Ligand Expos:MSE Link out to SuperLigands:MSE Link out to SuperHapten:MSE 2D
     
     
  •  
    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:   Aller, P.,   Rould, M.A.,   Hogg, M.,   Wallace, S.S.,   Doublie, S.

    Deposition:   2006-09-06
    Release:   2007-01-09
    Last Modified (REVDAT):   2010-01-12
     
     
  •  
    Move Section Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Experimental Data:   Download Structure Factors  [ EDS External Link to EDS ]
    View a histogram of Resolution Resolution[Å]: 2.65
    R-Value: 0.229 (work)
    R-Free: 0.281
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 132.61 α = 90.00 
    b = 122.63 β = 96.31 
    c = 168.70 γ = 90.00