3P4J

Ultra-high resolution structure of d(CGCGCG)2 Z-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.55 Å
  • R-Value Free: 0.085 
  • R-Value Work: 0.078 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.

Brzezinski, K.Brzuszkiewicz, A.Dauter, M.Kubicki, M.Jaskolski, M.Dauter, Z.

(2011) Nucleic Acids Res. 39: 6238-6248

  • DOI: 10.1093/nar/gkr202
  • Also Cited By: 4R15, 5EBI, 5JZQ

  • PubMed Abstract: 
  • The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DN ...

    The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.


    Organizational Affiliation

    Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.55 Å
  • R-Value Free: 0.085 
  • R-Value Work: 0.078 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.880α = 90.00
b = 31.420β = 90.00
c = 43.900γ = 90.00
Software Package:
Software NamePurpose
SHELXrefinement
SHELXLrefinement
SCALEPACKdata scaling
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Refinement description
  • Version 1.2: 2017-11-08
    Type: Refinement description