439D

5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.

Perbandt, M.Vallazza, M.Lippmann, C.Betzel, C.Erdmann, V.A.

(2001) Acta Crystallogr.,Sect.D 57: 219-224


  • PubMed Abstract: 
  • The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously un ...

    The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G.C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G.U wobble base pairs in tandem conformation, with the purines forming a so-called 'cross-strand G stack'.


    Organizational Affiliation

    Institute of Medical Biochemistry and Molecular Biology, University Hospital Eppendorf, c/o DESY Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')A8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')B8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 41.969α = 90.00
b = 41.969β = 90.00
c = 127.137γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance