3Q5C

Crystal structure of four-way junction with sticky end


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

Venkadesh, S.Mandal, P.K.Gautham, N.

(2011) Biochem Biophys Res Commun 407: 548-551

  • DOI: https://doi.org/10.1016/j.bbrc.2011.03.056
  • Primary Citation of Related Structures:  
    3Q5C

  • PubMed Abstract: 

    We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5Å. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.


  • Organizational Affiliation

    CAS in Crystallography and Biophysics, University of Madras, Chennai 600 025, India.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')
A, B, C, D
10N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.64α = 112.77
b = 33.841β = 90
c = 40.4γ = 110.44
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description