1KD4

The Crystal Structure of r(GGUCACAGCCC)2, Barium form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.203 

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.,Sect.D 59: 423-432

  • Primary Citation of Related Structures:  

  • 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 RNA ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'A,B11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.203 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 39.990α = 90.00
b = 39.990β = 90.00
c = 52.620γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CCP4data scaling
CNSphasing
DENZOdata reduction
Scalepack/Truncatedata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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