1P1Y

Crystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a continuous three-dimensional DNA lattice.

Paukstelis, P.J.Nowakowski, J.Birktoft, J.J.Seeman, N.C.

(2004) Chem.Biol. 11: 1119-1126

  • DOI: 10.1016/j.chembiol.2004.05.021
  • Also Cited By: 4RO4, 4RO7, 4RO8, 4ROG, 4ROK, 4RON, 4ROO, 4ROY, 4ROZ, 4RP0, 4RP1, 4RP2

  • PubMed Abstract: 
  • DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure c ...

    DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels that appear large enough to allow 3'-linked guest molecules into the crystal. We have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs, like those described here, may present a new tool in structural DNA nanotechnology.


    Organizational Affiliation

    Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA. paul@intron.icmb.utexas.edu




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'X13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
X
DNA LINKINGC9 H12 Br N2 O8 PDU
CBR
Query on CBR
X
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 40.630α = 90.00
b = 40.630β = 90.00
c = 55.270γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-02
    Type: Non-polymer description