122D

DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.

Hahn, M.Heinemann, U.

(1993) Acta Crystallogr.,Sect.D 49: 468-477

  • DOI: 10.1107/S0907444993004858
  • Primary Citation of Related Structures:  123D

  • PubMed Abstract: 
  • In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267, 7332-7341], the crystal structure of the double-stranded B-DNA decamer d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma structure amplitudes in the resolution ...

    In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267, 7332-7341], the crystal structure of the double-stranded B-DNA decamer d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma structure amplitudes in the resolution range 8-1.7 A. This structure has now been re-refined against the same diffraction data using either TNT or X-PLOR in order to determine to what extent the resulting DNA conformations would differ and to examine the suitability of these programs for the refinement of oligonucleotide structures. The R value from the NUCLSQ refinement could not be reached with either TNT or X-PLOR, although both programs yield reasonably refined DNA models showing root-mean-square deviations against the NUCLSQ model of the decamer duplex of 0.25 and 0.32 A, respectively. Some derived local structure parameters differ depending on the refinement procedure used. This holds true for several exocyclic torsion angles of the sugar-phosphate backbone, whereas sugar puckers as well as helical and base-pair stacking parameters are only weakly influenced. A subset of 15 solvent sites with low temperature factors is conserved in all three models.


    Related Citations: 
    • Crystallographic Study of One Turn of G/c-Rich B-DNA
      Heinemann, U.,Alings, C.
      (1989) J.Mol.Biol. 210: 369
    • C-C-A-G-G-C-M5C-T-G-G: Helical Fine Structure, Hydration, and Comparison with C-C-A-G-G-C-C-T-G-G
      Heinemann, U.,Hahn, M.
      (1992) J.Biol.Chem. 267: 7332
    • Double Helix Conformation, Groove Dimensions and Ligand Binding Potential of a G/C-Stretch in B-DNA
      Heinemann, U.,Alings, C.,Bansal, M.
      (1992) Embo J. 11: 1931
    • The Conformation of a B-DNA Decamer Is Mainly Determined by Its Sequence and Not by Crystal Environment
      Heinemann, U.,Alings, C.
      (1991) Embo J. 10: 35


    Organizational Affiliation

    Institut für Kristallographie, Freie Universität, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')A,B10N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
A, B
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 53.770α = 90.00
b = 53.770β = 90.00
c = 34.350γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance