137D

A-DNA DECAMER D(GCGGGCCCGC)-ORTHORHOMBIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures.

Ramakrishnan, B.Sundaralingam, M.

(1993) Biochemistry 32: 11458-11468

  • DOI: 10.1021/bi00093a025
  • Primary Citation of Related Structures:  
    137D, 138D

  • PubMed Abstract: 
  • We have determined the structure of the A-DNA decamer d(GCGGGCCCGC) in two crystal forms, orthorhombic and hexagonal, at 1.7- and 1.8-A resolution, respectively. In the orthorhombic form, the fifth guanine residue has nearly trans-trans conformations for the alpha-gamma backbone torsions, as in the isomorphous orthorhombic structure d(CCCGGCCGGG) [Ramakrishnan, B ...

    We have determined the structure of the A-DNA decamer d(GCGGGCCCGC) in two crystal forms, orthorhombic and hexagonal, at 1.7- and 1.8-A resolution, respectively. In the orthorhombic form, the fifth guanine residue has nearly trans-trans conformations for the alpha-gamma backbone torsions, as in the isomorphous orthorhombic structure d(CCCGGCCGGG) [Ramakrishnan, B., & Sundaralingam, M. (1993) J. Mol. Biol. 231, 431-444]. However, in the hexagonal form, the eighth cytosine residue adopts the trans-trans conformations for the backbone alpha-gamma torsions, as in the isomorphous hexagonal structure d(ACCGGCCGGT) [Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., van der Marel, G. A., van Boom, J. H., Rich, A., & Wang, A. H.-J. (1989) Eur. J. Biochem. 181, 295-307]. Even though the average helix and base-pair parameters are nearly the same in the two polymorphous crystal forms having the same sequence, many of the base-dependent local helix parameters are quite different. However, in the isomorphous crystal forms, in spite of the differing base sequences, the local helix and base-pair parameters of the duplexes are nearly the same. This indicates that, in crystals, the local conformation of a DNA structure is affected severely by the crystal packing environment rather than by the base sequence.


    Organizational Affiliation

    Department of Chemistry, Ohio State University, Columbus 43210-1002.



Macromolecules
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3')A, B10N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.70 Å
    • R-Value Work: 0.185 
    • R-Value Observed: 0.185 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 24.9α = 90
    b = 44.84β = 90
    c = 47.97γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1994-01-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance