426D

THE STRUCTURE OF MOST STUDIED DNA FRAGMENT CHANGES UNDER THE INFLUENCE OF IONS: A NEW PACKING OF D(CGCGAATTCGCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the most studied DNA fragment changes under the influence of ions: a new packing of d(CGCGAATTCGCG).

Liu, J.Malinina, L.Huynh-Dinh, T.Subirana, J.A.

(1998) FEBS Lett. 438: 211-214


  • PubMed Abstract: 
  • The title oligonucleotide and many related dodecamers have been extensively studied alone and as DNA-drug complexes. In practically all cases they were found to crystallize in the same space group, stabilized by interactions among the terminal guanin ...

    The title oligonucleotide and many related dodecamers have been extensively studied alone and as DNA-drug complexes. In practically all cases they were found to crystallize in the same space group, stabilized by interactions among the terminal guanine bases. Here we report new packing interactions (R3) in the presence of Ca2+. The oligonucleotides interact by placing their terminal guanines in the narrow groove of a neighbor molecule, an interaction which had never been found in dodecamers.


    Organizational Affiliation

    Department d'Enginyeria Química, Universitat Politènica de Catalunya, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 41.960α = 90.00
b = 41.960β = 90.00
c = 101.400γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance