1D57

ALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE STRUCTURE OF THE B-DNA DECAMER C-G-A-T-A-T-A-T-C-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G.

Yuan, H.Quintana, J.Dickerson, R.E.

(1992) Biochemistry 31: 8009-8021

  • Primary Citation of Related Structures:  1D56

  • PubMed Abstract: 
  • The X-ray crystal structure of the decamer C-G-A-T-A-T-A-T-C-G has been solved with two contrasting cations, Ca2+ and Mg2+. Crystals with calcium are space group P2(1)2(1)2(1), cell dimensions a = 38.76 A, b = 40.06 A, and c = 33.73 A, and diffract t ...

    The X-ray crystal structure of the decamer C-G-A-T-A-T-A-T-C-G has been solved with two contrasting cations, Ca2+ and Mg2+. Crystals with calcium are space group P2(1)2(1)2(1), cell dimensions a = 38.76 A, b = 40.06 A, and c = 33.73 A, and diffract to 1.7-A resolution. Crystals with magnesium have the same space group, cell dimensions a = 38.69 A, b = 39.56 A, and c = 33.64 A, and diffract to 2.0 A. Their structures were solved independently by molecular replacement, beginning with idealized Arnott B-DNA geometry. The calcium structure refined to R = 17.8% for the 3683 reflections greater than 2 sigma, with 404 DNA atoms, 95 solvent peaks, and 1 Ca(H2O)7(2+) ion. The magnesium structure refined to R = 16.5% for the 1852 reflections greater than 2 sigma, with 404 DNA atoms, 62 solvent peaks, and 1 Mg(H2O)6(2+) ion. The two structures are virtually identical and are isostructural with C-G-A-T-C-G-A-T-C-G [Grzeskowiak et al. (1991) J. Biol. Chem. 266, 8861-8883] and C-G-A-T-T-A-A-T-C-G [Quintana et al. (1992) J. Mol. Biol. 225, 375-395]. Comparison of C-G-A-T-A-T-A-T-C-G with C-G-C-A-T-A-T-A-T-G-C-G [Yoon et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 6332-6336] shows that the expected alternation of twist angles is found in the central A-T-A-T-A-T region of the decamer (A-T small, T-A large), but the minor groove remains wide at the center, rather than narrow. Minor groove narrowing is produced, in these two structures, not by overwinding of the helix, but by an increase in base pair propeller. This analysis confirms the concept that poly(dA-dT).poly(dA-dT) is polymorphous, with different local conformations possible in different local environments.


    Related Citations: 
    • The Structure of B-Helical C-G-A-T-C-G-A-T-C-G and Comparison with C-C-A-A-C-G-T-T-G-G. The Effect of Base Pair Reversals
      Grzeskowiak, K.,Yanagi, K.,Prive, G.G.,Dickerson, R.E.
      (1991) J.Biol.Chem. 266: 8861
    • Analysis of Local Helix Geometry in Three B-DNA Decamers and Eight Dodecamers
      Yanagi, K.,Prive, G.G.,Dickerson, R.E.
      (1991) J.Mol.Biol. 217: 201


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3')A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.690α = 90.00
b = 39.560β = 90.00
c = 33.640γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-09-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance