1S23

Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

DNA variability in five crystal structures of d(CGCAATTGCG).

Valls, N.Wright, G.Steiner, R.A.Murshudov, G.N.Subirana, J.A.

(2004) Acta Crystallogr D Biol Crystallogr 60: 680-685

  • DOI: https://doi.org/10.1107/S0907444904002896
  • Primary Citation of Related Structures:  
    1S23

  • PubMed Abstract: 

    The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.


  • Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, E-08028 Barcelona, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.22α = 90
b = 44.359β = 90
c = 52.336γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description