401D

STRUCTURE OF A DNA IN LOW SALT CONDITIONS D(GACCGCGGTC)

  • Classification: DNA

  • Deposited: 1998-06-02 Released: 1998-07-06 
  • Deposition Author(s): Luo, M., Finley, J.B.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGGTC).

Finley, J.B.Luo, M.

(1998) Nucleic Acids Res. 26: 5719-5727

  • Primary Citation of Related Structures:  348D, 349D

  • PubMed Abstract: 
  • The X-ray crystal structure of the DNA decamer d(GACCGCGGTC), containing half the human papilloma virus E2 binding site, has been solved from two crystals grown at different ionic conditions (50 mM MgCl2and 50 mM spermine or 1.56 mM MgCl2and 1.56 mM ...

    The X-ray crystal structure of the DNA decamer d(GACCGCGGTC), containing half the human papilloma virus E2 binding site, has been solved from two crystals grown at different ionic conditions (50 mM MgCl2and 50 mM spermine or 1.56 mM MgCl2and 1.56 mM spermine). Despite the variation in salt concentration, the two DNA structures are in a very similar, A-type DNA conformation, with helical axes curving towards the major groove. Although the salt concentrations do not effect the helical parameters or hydration to a large degree, there is a change in the overall helical curvature; 18 degrees and 31 degrees for the low and high salt structures, respectively. This curvature appears to be sequence specific and biologically relevant when compared with similar DNA structures, including the E2 binding site of a protein-DNA complex.


    Organizational Affiliation

    Center for Macromolecular Crystallography, Department of Microbiology, University of Alabama-Birmingham, Birmingham, AL 35294-0005, USA. jfinley@orion.cmc.uab.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')A10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.219 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 38.444α = 90.00
b = 38.444β = 90.00
c = 80.175γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-06-02 
  • Released Date: 1998-07-06 
  • Deposition Author(s): Luo, M., Finley, J.B.

Revision History 

  • Version 1.0: 1998-07-06
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance