5ANA

THE CRYSTAL STRUCTURE OF D(GTACGTAC) AT 2.25 ANGSTROMS RESOLUTION. ARE THE A-DNA'S ALWAYS UNWOUND APPROXIMATELY 10 DEGREES AT THE C-G STEPS

  • Classification: DNA

  • Deposited: 1989-10-31 Released: 1990-04-15 
  • Deposition Author(s): Takusagawa, F.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å

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Literature

The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps

Takusagawa, F.

(1990) J.Biomol.Struct.Dyn. 7: 795-809

  • DOI: 10.1080/07391102.1990.10508524

  • PubMed Abstract: 
  • The structure of the self-complementary octamer d(GTACGTAC) has been analyzed by a single crystal X-ray diffraction method at 2.25 A resolution. The crystallographic R factor was 0.184 for all 1233 reflections at this resolution. In spite of the alte ...

    The structure of the self-complementary octamer d(GTACGTAC) has been analyzed by a single crystal X-ray diffraction method at 2.25 A resolution. The crystallographic R factor was 0.184 for all 1233 reflections at this resolution. In spite of the alternating purine-pyrimidine sequence, d(GTACGTAC) adopts the A-form conformation rather than the left-handed Z-form. The average helix twist and the mean rise per base pair are 32.1 degrees and 3.18 A, respectively. The d(GTACGTAC) helix is characterized by a wide open major groove and small base-pair tilt (9.7 degrees). The partial unwinding of the helix is observed only at the central pyrimidine-purine C-G step, but not at the other pyrimidine-purine T-A steps. Based on this study and six other X-ray studies, we propose a hypothesis that the A-DNA's are always unwound approximately 10 degrees at the C-G steps. Significant differences in base-pair stacking modes are seen between the purine-pyrimidine step and the pyrimidine-purine step. All deoxyribose rings adopt the C3'-endo conformation. All backbone torsion angles fall into the range expected for the A-DNA form, except for the nucleotide G5, whose alpha and gamma torsion angles adopt the trans, trans conformation instead of the common gauche-, gauche+ conformation.


    Organizational Affiliation

    Department of Chemistry, University of Kansas, Lawrence 66045.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')A8N/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: 2.25 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.320α = 90.00
b = 42.320β = 90.00
c = 25.044γ = 90.00
Software Package:
Software NamePurpose
CORELSrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1989-10-31 
  • Released Date: 1990-04-15 
  • Deposition Author(s): Takusagawa, F.

Revision History 

  • Version 1.0: 1990-04-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance