464D

DISORDER AND TWIN REFINEMENT OF RNA HEPTAMER DOUBLE HELIX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Disorder and twin refinement of RNA heptamer double helices.

Mueller, U.Muller, Y.A.Herbst-Irmer, R.Sprinzl, M.Heinemann, U.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1405-1413

  • DOI: 10.1107/s0907444999007441
  • Primary Citation of Related Structures:  
    464D, 466D

  • PubMed Abstract: 
  • An RNA helix with seven base pairs which was derived from the acceptor stem of Escherichia coli tRNA(Ala), rGGGGCUA.rUAGCUCC (ALA(wt)), as well as a variant, rGGGGCUA.rUAGCCCC (ALA(C70)), in which the single G.U wobble base pair of ALA(wt) was replac ...

    An RNA helix with seven base pairs which was derived from the acceptor stem of Escherichia coli tRNA(Ala), rGGGGCUA.rUAGCUCC (ALA(wt)), as well as a variant, rGGGGCUA.rUAGCCCC (ALA(C70)), in which the single G.U wobble base pair of ALA(wt) was replaced by G.C, crystallize in space group C2. Both non-isomorphic crystal forms display a complex packing pattern, which can be described alternatively as disorder or pseudo-merohedral twinning. The structure of ALA(wt) was determined by SIRAS phasing using an isomorphous iodine derivative, rGGGGCi(5)UA.rUAGCUCC (ALA(I)). All three RNA structures were subsequently subjected to twin refinement in space group P1, using anisotropic thermal displacement parameters at resolutions of 1.16, 1.23 and 1.4 A for ALA(wt), ALA(I) and ALA(C70), respectively. Alternatively, the structure of ALA(wt) was refined in space group C2 assuming twofold disorder of the molecular orientation. The refined structures are of reasonable quality according to all available indicators. There are no systematic differences between the molecular models resulting from twin refinement and disorder refinement.


    Organizational Affiliation

    Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')A, C7N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')B, D7N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SR
      Query on SR

      Download CCD File 
      B
      STRONTIUM ION
      Sr
      PWYYWQHXAPXYMF-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download CCD File 
      B
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.23 Å
      • R-Value Free: 0.193 
      • R-Value Work: 0.127 
      • R-Value Observed: 0.129 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 26.375α = 110.37
      b = 28.995β = 96.62
      c = 28.995γ = 96.62
      Software Package:
      Software NamePurpose
      SHELXL-97refinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1999-08-16
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance