2A2T

crystal structure of d(AAATATTT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a DNA duplex with all-AT base pairs.

Valls, N.Richter, M.Subirana, J.A.

(2005) Acta Crystallogr.,Sect.D 61: 1587-1593

  • DOI: 10.1107/S0907444905029781

  • PubMed Abstract: 
  • The structure of the oligonucleotide duplex d(AAATATTT)(2) has been obtained in two crystal forms. In both cases the duplexes show Watson-Crick base pairs and are organized as a helical arrangement of stacked oligonucleotides. The helices contain eit ...

    The structure of the oligonucleotide duplex d(AAATATTT)(2) has been obtained in two crystal forms. In both cases the duplexes show Watson-Crick base pairs and are organized as a helical arrangement of stacked oligonucleotides. The helices contain either 11 duplexes in seven turns (form I) or 14 duplexes in nine turns (form II). As a result, the crystals have rather large unit cells. Such an organization of DNA duplexes has not been previously described in oligonucleotide crystal structures. The columns of stacked duplexes are organized in a pseudohexagonal arrangement. They do not show any direct lateral interactions; instead, these are indirectly mediated by shared and disordered hydrated ions. Such interactions are similar to those found in DNA fibres. The structural parameters of the individual base steps coincide with those found in other structures which contain CG terminal base pairs.


    Organizational Affiliation

    Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barclelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'A,G,B,H,C,I,D,J,E,K,F8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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D, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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Download CCD File 
E
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.272 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.623α = 90.00
b = 24.985β = 90.51
c = 82.139γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance