422D

5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the dodecamer r(GAUCACUUCGGU) with four 5'-overhang nucleotides.

Eswaramoorthy, S.Rao, S.T.Pan, B.Sundaralingam, M.

(2004) Acta Crystallogr.,Sect.D 60: 8-12


  • PubMed Abstract: 
  • The crystal structure of an RNA dodecamer, r(GAUCACUUCGGU), was solved at 2.6 A resolution by the molecular-replacement method and refined to an R(work) of 18.8% (R(free) = 22.8%) using 2494 reflections. The dodecamer crystallized in the monoclinic s ...

    The crystal structure of an RNA dodecamer, r(GAUCACUUCGGU), was solved at 2.6 A resolution by the molecular-replacement method and refined to an R(work) of 18.8% (R(free) = 22.8%) using 2494 reflections. The dodecamer crystallized in the monoclinic space group C2, with unit-cell parameters a = 71.34, b = 39.98, c = 32.47 A, beta = 104.7 degrees and two independent strands in the asymmetric unit. The dodecamer adopts an octamer duplex structure with four 5'-overhang residues (G1A2U3C4), which form Watson-Crick base pairs with another four 5'-overhang residues of a symmetry-related duplex. The octamer duplex (ACUUCGGU) contains at its center four mismatched base pairs flanked by two Watson-Crick base pairs. The mismatched bases form two G.U wobble base pairs at the ends and two U.C base pairs at the center, with one base-base hydrogen bond N4(C).O4(U) and a water bridge connecting the N(3) of the cytosine and uridine. The present study reinforces the concept of the stability of the conformation of UUCG in RNA double-helical structures.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'A,B12N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.340α = 90.00
b = 39.980β = 104.70
c = 32.470γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance