3LLN

Comparison between the orthorhombic an tetragonal form of the heptamer sequence d(GCG(xT)GCG)/d(CGCACGC).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


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Literature

Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC)

Robeyns, K.Herdewijn, P.Van Meervelt, L.

(2010) Acta Crystallogr.,Sect.F 66: 1028-1031

  • DOI: 10.1107/S1744309110031696

  • PubMed Abstract: 
  • Cyclohexene nucleic acid (CeNA) building blocks can be introduced into natural DNA sequences without a large conformational influence because of the ability of the six-membered sugar ring to mimic both the C2'-endo and C3'-endo conformations of the n ...

    Cyclohexene nucleic acid (CeNA) building blocks can be introduced into natural DNA sequences without a large conformational influence because of the ability of the six-membered sugar ring to mimic both the C2'-endo and C3'-endo conformations of the naturally occurring ribofuranose sugar ring. The non-self-complementary DNA sequence d[GCG(xT)GCG]/d(CGCACGC) with one incorporated CeNA (xT) moiety crystallizes in two forms: orthorhombic and tetragonal. The tetragonal form, which diffracts to 3 A resolution, is a kinetically stable polymorph of the orthorhombic form [Robeyns et al. (2010), Artificial DNA, 1, 1-7], which diffracts to 1.17 A resolution and is the thermodynamically stable form of the CeNA-incorporated duplex. Here, the two structures are compared, with special emphasis on the differences in crystal packing and the irreversible conversion of the kinetic form into the high-resolution diffracting thermodynamic form.


    Related Citations: 
    • Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG).
      Robeyns, K.,Herdewijn, P.,Van Meervelt, L.
      (2008) Nucleic Acids Res. 36: 1407
    • Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.
      Robeyns, K.,Herdewijn, P.,Van Meervelt, L.
      (2008) J.Am.Chem.Soc. 130: 1979
    • Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA
      Robeyns, K.,Herdewijn, P.,Van Meervelt, L.
      (2010) Artificial DNA 1: 1


    Organizational Affiliation

    Department of Chemistry, Biomolecular Architecture and BioMacS, Katholieke Universiteit Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3')A7N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*CP*GP*C)-3')B7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
XTR
Query on XTR
A
DNA linkingC12 H17 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 25.482α = 90.00
b = 25.482β = 90.00
c = 81.147γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance