2HBN

Crystallization of the Tl+-form of the Oxytricha nova G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex.

Gill, M.L.Strobel, S.A.Loria, J.P.

(2006) Nucleic Acids Res 34: 4506-4514

  • DOI: 10.1093/nar/gkl616
  • Primary Citation of Related Structures:  
    2HBN

  • PubMed Abstract: 
  • The crystal structure of the Tl+ form of the G-quadruplex formed from the Oxytricha nova telomere sequence, d(G4T4G4), has been solved to 1.55 A. This G-quadruplex contains five Tl+ ions, three of which are interspersed between adjacent G-quartet pla ...

    The crystal structure of the Tl+ form of the G-quadruplex formed from the Oxytricha nova telomere sequence, d(G4T4G4), has been solved to 1.55 A. This G-quadruplex contains five Tl+ ions, three of which are interspersed between adjacent G-quartet planes and one in each of the two thymine loops. The structure displays a high degree of similarity to the K+ crystal structure [Haider et al. (2002), J. Mol. Biol., 320, 189-200], including the number and location of the monovalent cation binding sites. The highly isomorphic nature of the two structures, which contain such a large number of monovalent binding sites (relative to nucleic acid content), verifies the ability of Tl+ to mimic K+ in nucleic acids. Information from this report confirms and extends the assignment of 205Tl resonances from a previous report [Gill et al. (2005), J. Am. Chem. Soc., 127, 16 723-16 732] where 205Tl NMR was used to study monovalent cation binding to this G-quadruplex. The assignment of these resonances provides evidence for the occurrence of conformational dynamics in the thymine loop region that is in slow exchange on the 205Tl timescale.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'A, B, C, D12N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TL
    Query on TL

    Download CCD File 
    A, B, C, D
    THALLIUM (I) ION
    Tl
    ZLUSCZLCHQSJRU-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.248 
    • R-Value Work: 0.226 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 27.375α = 90
    b = 48.21β = 90
    c = 96.198γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2006-09-19
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-10-18
      Changes: Refinement description