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: 2.4 Å

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


  • 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 15 ...

    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.,Sect.D 49: 418


    Organizational Affiliation

    Institut für Biochemie, Freie Universität Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')A12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')B12N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 30.100α = 90.00
b = 30.100β = 90.00
c = 86.800γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
DENZOdata reduction
AMoREphasing
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-10
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-14
    Type: Data collection, Experimental preparation