353D

CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.

Betzel, C.Lorenz, S.Furste, J.P.Bald, R.Zhang, M.Schneider, T.R.Wilson, K.S.Erdmann, V.A.

(1994) FEBS Lett 351: 159-164

  • DOI: 10.1016/0014-5793(94)00834-5
  • Primary Citation of Related Structures:  
    353D

  • PubMed Abstract: 
  • This is the first high resolution crystal structure of an RNA molecule made by solid phase chemical synthesis and representing a natural RNA. The structure of the domain A of Thermus flavus ribosomal 5S RNA is refined to R = 18% at 2.4 A including 159 solvent molecules ...

    This is the first high resolution crystal structure of an RNA molecule made by solid phase chemical synthesis and representing a natural RNA. The structure of the domain A of Thermus flavus ribosomal 5S RNA is refined to R = 18% at 2.4 A including 159 solvent molecules. Most of the 2'-hydroxyl groups as well as the phosphate oxygens are involved either in specific hydrogen bonds in intermolecular contacts or to solvent molecules. The two U-G and G-U base-pairs are stabilized by H-bonds supplied via three water molecules to compensate for the lack of base-pair hydrogen bonds. The structure shows for the first time in detail the importance of highly ordered internal water in stabilizing an RNA structure.


    Related Citations: 
    • Structure of Domain A of Thermus flavus 5S rRNA at 2.3 A Resolution. Comparison of Nearest Neighbor Parameters for Mismatches and the Influence of Solvent
      Perbandt, M., Lorenz, S., Betzel, C., Erdmann, V.A.
      () To be published --: --
    • Crystallization and Preliminary Diffraction Studies of the Chemically Synthesized Domain A of Thermus flavus 5S rRNA: An Dodecamer Double Helix
      Lorenz, S., Furste, J., Bald, R., Zhang, M., Raderschall, E., Betzel, C., Dauter, Z., Wilson, K.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 418

    Organizational Affiliation

    Institut für Biochemie, Freie Universität Berlin, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')A 12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')B 12N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.180 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.1α = 90
b = 30.1β = 90
c = 86.8γ = 90
Software Package:
Software NamePurpose
AMoREphasing
NUCLSQrefinement
XDSdata reduction
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-11-10
    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: 2018-02-14
    Changes: Data collection, Experimental preparation