4R48

Racemic crystal structure of a calcium-bound DNA four-way junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


This is version 1.2 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, 4R47, 4R48, 4R49, 4R4A, 4R4D

  • 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   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'A, B10synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.289 
  • Space Group: C 1 2/c 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.95α = 90
b = 23.355β = 115.47
c = 72.907γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
d*TREKdata scaling

Structure Validation

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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
  • Version 1.2: 2019-08-28
    Changes: Data collection, Derived calculations