4R4D

Racemic crystal structure of a magnesium-bound B-DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Racemic DNA crystallography.

Mandal, P.K.Collie, G.W.Kauffmann, B.Huc, I.

(2014) Angew Chem Int Ed Engl 53: 14424-14427

  • DOI: 10.1002/anie.201409014
  • Primary Citation of Related Structures:  
    4R44, 4R45, 4R4A, 4R4D, 4R47, 4R48, 4R49

  • PubMed Abstract: 
  • Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides ...

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.


    Organizational Affiliation

    Université de Bordeaux, CBMN, UMR5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600 Pessac (France); CNRS, CBMN, UMR5248.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'A, B, C, D10synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.29 Å
    • R-Value Free: 0.311 
    • R-Value Work: 0.269 
    • R-Value Observed: 0.271 
    • Space Group: P -1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 31.61α = 70.76
    b = 32.951β = 80.77
    c = 46.25γ = 73.77
    Software Package:
    Software NamePurpose
    DNAdata collection
    PHASERphasing
    REFMACrefinement
    XDSdata reduction
    d*TREKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-11-12
      Type: Initial release
    • Version 1.1: 2015-01-14
      Changes: Database references