5EZF

Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.296 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.

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

(2016) Nucleic Acids Res. 44: 5936-5943

  • DOI: 10.1093/nar/gkw367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by ...

    It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 Ã…), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.


    Related Citations: 
    • Racemic DNA Crystallography
      Mandal, P.K.,Collie, G.W.,Kauffmann, B.,Huc, I.
      (2014) Angew. Chem. Int. Ed. 53: 14424


    Organizational Affiliation

    Université de Bordeaux, CBMN (UMR5248), Pessac 33600, France CNRS, CBMN (UMR5248), Pessac 33600, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Pribnow box template strandA12synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
Complementary strandB12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.296 
  • Space Group: P b c a
Unit Cell:
Length (Å)Angle (°)
a = 41.736α = 90.00
b = 39.329β = 90.00
c = 65.713γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFranceERC-2012-AdG-320892

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references