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 (Depositor), 0.080 (DCC) 
  • R-Value Work: 
    0.078 (Depositor), 0.080 (DCC) 
  • R-Value Observed: 
    0.078 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1093/nar/gkr202
  • Primary Citation of Related Structures:  
    3P4J

  • 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-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 nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
A, B
6N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
C [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.55 Å
  • R-Value Free:  0.085 (Depositor), 0.080 (DCC) 
  • R-Value Work:  0.078 (Depositor), 0.080 (DCC) 
  • R-Value Observed: 0.078 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 17.88α = 90
b = 31.42β = 90
c = 43.9γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXLrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Refinement description
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description