181D

SEQUENCE-DEPENDENT MICROHETEROGENEITY OF Z-DNA: THE CRYSTAL AND MOLECULAR STRUCTURES OF D(CACGCG).D(CGCGTG) AND D(CGCACG).D(CGTGCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sequence-dependent microheterogeneity of Z-DNA: the crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG).

Sadasivan, C.Gautham, N.

(1995) J.Mol.Biol. 248: 918-930

  • DOI: 10.1006/jmbi.1995.9894
  • Primary Citation of Related Structures:  180D

  • PubMed Abstract: 
  • We have solved and refined the crystal structures of the first two non-self-complementary hexadeoxyribonucleotide duplexes with Watson-Crick base pairs, namely d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG). Both the hexamers crystallize in the left-han ...

    We have solved and refined the crystal structures of the first two non-self-complementary hexadeoxyribonucleotide duplexes with Watson-Crick base pairs, namely d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG). Both the hexamers crystallize in the left-handed Z-DNA conformation. The packing of the molecules is similar in the two crystals: the hexamers are stacked on top of each other to form columns of infinite length, which are arranged in a close-packed hexagonal pattern. In spite of the similar packing, crystals of the first duplex belong to the space group P2(1)2(1)2(1), isomorphous to previous Z-DNA hexamers, while crystals of the other duplex belong to the space group P2(1), which has not been observed before in this context. The molecular structures of the two duplexes are also different. The first is very similar in conformation to the other Z-DNA hexamers and to the idealized ZI model. The other duplex shows large differences in the stacking and the relative disposition of its bases, leading to its possible classification as a novel Z-DNA variant. We conclude that the differences in the structure under similar environmental conditions point to a sequence-dependent plasticity in the DNA molecule which is visible even under close-packed conditions.


    Related Citations: 
    • Plasticity of Z-DNA as Observed in the Crystal Structures of Non-Selfcomplementary Hexanucleotides
      Sadasivan, C.,Gautham, N.
      () TO BE PUBLISHED --: --
    • Space Group Degeneracy in the Packing of a Non-Selfcomplementary Z-DNA Hexamer
      Sadasivan, C.,Karthe, P.,Gautham, N.
      (1994) Acta Crystallogr.,Sect.D 50: 192


    Organizational Affiliation

    Department of Crystallography and Biophysics, University of Madras, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')A6N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')B6N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.760α = 90.00
b = 30.960β = 90.00
c = 44.750γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-19
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance