1WQZ

Complicated water orientations in the minor groove of B-DNA decamer D(CCATTAATGG)2 observed by neutron diffraction measurements


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements

Arai, S.Chatake, T.Ohhara, T.Kurihara, K.Tanaka, I.Suzuki, N.Fujimoto, Z.Mizuno, H.Niimura, N.

(2005) Nucleic Acids Res 33: 3017-3024

  • DOI: 10.1093/nar/gki616
  • Primary Citation of Related Structures:  
    1WQY, 1WQZ

  • PubMed Abstract: 
  • It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex ...

    It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.


    Organizational Affiliation

    Neutron Science Research Center, Japan Atomic Energy Research Institute 2-4 Shirakatashirane, Tokai, Ibaraki 319-1195, Japan.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3'A, B 10synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.9α = 90
b = 32.9β = 90
c = 96.1γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2018-07-04
    Changes: Data collection, Source and taxonomy