192D

RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recombination-like structure of d(CCGCGG).

Malinina, L.Urpi, L.Salas, X.Huynh-Dinh, T.Subirana, J.A.

(1994) J.Mol.Biol. 243: 484-493

  • DOI: 10.1006/jmbi.1994.1674

  • PubMed Abstract: 
  • We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the ...

    We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*CP*GP*G)-3')A,B6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Work: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 34.330α = 90.00
b = 44.040β = 90.00
c = 38.270γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance