1QC1

CRYSTAL STRUCTURE OF THE SELF-FITTED B-DNA DECAMER D(CCGCCGGCGG)

  • Classification: DNA

  • Deposited: 1999-05-14 Released: 1999-05-28 
  • Deposition Author(s): Timsit, Y., Moras, D.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

DNA self-fitting: the double helix directs the geometry of its supramolecular assembly

Timsit, Y.Moras, D.

(1994) EMBO J. 13: 2737-2746


  • PubMed Abstract: 
  • Groove-backbone interaction is a natural and biologically relevant mechanism for the specific assembly of B-DNA double helices. Crystal engineering and crystal packing analysis of oligonucleotides of different sizes and sequences reveal that the sequ ...

    Groove-backbone interaction is a natural and biologically relevant mechanism for the specific assembly of B-DNA double helices. Crystal engineering and crystal packing analysis of oligonucleotides of different sizes and sequences reveal that the sequence-dependent self-fitting of B-DNA helices is a dominant constraint for their ordered assembly. It can override the other intermolecular interactions and impose the overall geometry of the packing. Analysis of experimental examples of architectural motifs formed by the geometric combination of self-fitted DNA segments leads to general rules for DNA assembly. Like a directing piece for a supramolecular 'construction set', the double helix imposes a limited number of geometric solutions. These basic architectural constraints could direct, in a codified manner, the formation of higher-order structures. DNA architectural motifs exhibit new structural and electrostatic properties which could have some implications for their molecular recognition by proteins acting on DNA.


    Related Citations: 
    • Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations
      Timsit, Y.,Shatzky-Schwartz, M.,Shakked, Z.
      (1999) J.Biomol.Struct.Dyn. 16: 775


    Organizational Affiliation

    UPR de Biologie Structurale, CNRS, Institut de Biologie Mol├ęculaire et Cellulaire, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3'A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 53.700α = 90.00
b = 53.700β = 90.00
c = 45.000γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement
X-GENdata scaling
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-05-14 
  • Released Date: 1999-05-28 
  • Deposition Author(s): Timsit, Y., Moras, D.

Revision History 

  • Version 1.0: 1999-05-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description