3U89

Crystal structure of one turn of g/c rich b-dna revisited


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions.

Maehigashi, T.Hsiao, C.Woods, K.K.Moulaei, T.Hud, N.V.Williams, L.D.

(2012) Nucleic Acids Res. 40: 3714-3722

  • DOI: 10.1093/nar/gkr1168

  • PubMed Abstract: 
  • Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffr ...

    Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.


    Organizational Affiliation

    School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'A10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 32.136α = 90.00
b = 25.172β = 116.25
c = 34.094γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references
  • Version 1.2: 2012-10-17
    Type: Database references