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: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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This is version 1.4 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

  • DOI: https://doi.org/10.1016/s0014-5793(98)00436-0
  • Primary Citation of Related Structures:  
    361D

  • 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 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
MoleculeChains LengthOrganismImage
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, B
20N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.68α = 90
b = 42.68β = 90
c = 161.2γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description