4HW1

Multiple Crystal structures of an all-AT DNA dodecamer stabilized by weak interactions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Polymorphic crystal structures of an all-AT DNA dodecamer.

Acosta-Reyes, F.J.Subirana, J.A.Pous, J.Sanchez-Giraldo, R.Condom, N.Baldini, R.Malinina, L.Campos, J.L.

(2015) Biopolymers 103: 123-133

  • DOI: 10.1002/bip.22565
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organiza ...

    In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, 08028, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')A,B,C,D12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.262 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.431α = 90.00
b = 61.155β = 90.00
c = 80.601γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
ADSCdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references