4R45

Racemic crystal structure of a bimolecular DNA G-quadruplex (P-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 

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
  • Structures With Same Primary Citation

  • 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. ...

    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
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'A, B12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 
  • Space Group: P -1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.646α = 104.5
b = 28.3β = 94.19
c = 45.719γ = 113.42
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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