1EHV

A NEW CRYSTAL STRUCTURE FOR THE DODECAMER C-G-C-G-A-A-T-T-C-G-C-G: SYMMETRY EFFECTS ON SEQUENCE-DEPENDENT DNA STRUCTURE

  • Classification: DNA

  • Deposited: 2000-02-23 Released: 2000-07-14 
  • Deposition Author(s): Johansson, E.M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure.

Johansson, E.Parkinson, G.Neidle, S.

(2000) J.Mol.Biol. 300: 551-561

  • DOI: 10.1006/jmbi.2000.3907

  • PubMed Abstract: 
  • The dodecanucleotide d(CGCGAATTCGCG) has been crystallised in the space group P3(2)12, representing a new crystal form for this sequence. The structure has been solved by molecular replacement and refined at 1.8 A resolution. The present structure co ...

    The dodecanucleotide d(CGCGAATTCGCG) has been crystallised in the space group P3(2)12, representing a new crystal form for this sequence. The structure has been solved by molecular replacement and refined at 1.8 A resolution. The present structure contrasts with previous ones for this sequence since it is situated on a crystallographic 2-fold axis, and the crystal symmetry reflects the palindromic nature of this sequence. Some features accord with previous observations, notably that the minor groove is hydrated with a continuous spine of solvent. There is no evidence of alkali metal ions within this spine. The minor groove retains its narrow width, although it is now symmetric and extends over the A/T tract. Various base and base-pair morphological parameters have been examined. Their values do not show significant correlations with earlier reports, suggesting that crystal packing effects on them are more dominant than has been hitherto realised.


    Organizational Affiliation

    Institute of Cancer Research, CRC Biomolecular Structure Unit, Chester Beatty Laboratories, Fulham Road, London, SW3 6JB, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A12N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.238 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 26.390α = 90.00
b = 26.390β = 90.00
c = 98.780γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
MAR345data collection
X-PLORphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-02-23 
  • Released Date: 2000-07-14 
  • Deposition Author(s): Johansson, E.M.

Revision History 

  • Version 1.0: 2000-07-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description