1KD5

The Crystal Structure of r(GGUCACAGCCC)2 metal free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of r(GGUCACAGCCC)2.

Kacer, V.Scaringe, S.A.Scarsdale, J.N.Rife, J.P.

(2003) Acta Crystallogr D Biol Crystallogr 59: 423-432

  • DOI: 10.1107/s0907444902021911
  • Primary Citation of Related Structures:  
    1KD3, 1KD4, 1KD5

  • PubMed Abstract: 
  • Crystals of small RNAs, which regularly diffract to very high resolution, can often be readily obtained. Unfortunately, for some RNAs the conformations adopted in the crystalline form are different from those found in solution. For example, short RNAs that form hairpins in solution virtually never crystallize thus; rather, they form duplexes ...

    Crystals of small RNAs, which regularly diffract to very high resolution, can often be readily obtained. Unfortunately, for some RNAs the conformations adopted in the crystalline form are different from those found in solution. For example, short RNAs that form hairpins in solution virtually never crystallize thus; rather, they form duplexes. Nevertheless, these unintended structures have contributed greatly to the understanding of RNA structure. In a similar occurrence, the homodimer r(GGUCACAGCCC)(2) has been crystallized from an 11-mer/12-mer heteroduplex, r(GGCUGAAGUCCG)/r(GGUCACAGCCC). This surprising phenomenon was observed under a variety of crystallization conditions. The structure of the homoduplex was determined from crystals that differed in the precipitant used and the type of metal present. In all cases, the resulting homoduplexes contain ten base pairings, of which the central six are non-canonical pairings. In two of the variants, ordered metal-binding sites were observed: two equivalent octacoordinate Tl(+) sites in one and two equivalent nanocoordinate Ba(2+) sites in another.


    Organizational Affiliation

    Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0133, USA.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'A, B 11N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.388α = 90
b = 45.388β = 90
c = 51.499γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-96refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance