361D

CRYSTAL STRUCTURE OF DOMAIN E OF THERMUS FLAVUS 5S RRNA: A HELICAL RNA-STRUCTURE INCLUDING A TETRALOOP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of domain E of Thermus flavus 5S rRNA: a helical RNA structure including a hairpin loop.

Perbandt, M.Nolte, A.Lorenz, S.Bald, R.Betzel, C.Erdmann, V.A.

(1998) FEBS Lett. 429: 211-215


  • PubMed Abstract: 
  • The synthetic RNA fragment 5'-CUGGGCGG(GCGA)CCGCCUGG (nucleotides in parentheses indicate the loop region) corresponds to the natural sequence of domain E from nucleotides 79-97 of the Thermus flavus 5S rRNA including a hairpin loop. The RNA structur ...

    The synthetic RNA fragment 5'-CUGGGCGG(GCGA)CCGCCUGG (nucleotides in parentheses indicate the loop region) corresponds to the natural sequence of domain E from nucleotides 79-97 of the Thermus flavus 5S rRNA including a hairpin loop. The RNA structure determined at 3.0 A and refined to an R-value of 24.1% also represents the first X-ray structure GNRA tetraloop. The loop is in distinctly different conformation from other GNRA tetraloops analyzed by NMR. The conformation of the two molecules in the asymmetric unit is influenced and stabilized by specific intermolecular contacts. The structural features presented here give evidence for the ability of RNA molecules to adapt to specific environments.


    Organizational Affiliation

    Institut für Biochemie, Freie Universität Berlin, Germany.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3')A,B20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.241 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 42.680α = 90.00
b = 42.680β = 90.00
c = 161.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance