3CWT

Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxyinosine:Adenine Base Pair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA.

Bowman, B.R., Lee, S., Wang, S., Verdine, G.L.

(2008) Structure 16: 1166-1174

  • DOI: 10.1016/j.str.2008.04.012
  • Primary Citation of Related Structures:  
    3CWA, 3CW7, 3CVS, 3CVT, 3CWS, 3CWT, 3CWU

  • PubMed Abstract: 

    • The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences ...

    The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-3-methyladenine glycosylase 2 A, B, C, D282Escherichia coliMutation(s): 0 
Gene Names: alkA, aidA
EC: 3.2.2.21
Find proteins for P04395 (Escherichia coli (strain K12))
Explore P04395 
Go to UniProtKB:  P04395
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FI)P*DTP*DGP*DCP*DC)-3')E, G12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')F, H12N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.280 
      • R-Value Work: 0.239 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 75.748α = 90
      b = 101.478β = 93.72
      c = 103.113γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-09-02
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-10-25
        Changes: Refinement description