3L0U

The crystal structure of unmodified tRNAPhe from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of unmodified tRNAPhe from Escherichia coli

Byrne, R.T.Konevega, A.L.Rodnina, M.V.Antson, A.A.

(2010) Nucleic Acids Res. 38: 4154-4162

  • DOI: 10.1093/nar/gkq133

  • PubMed Abstract: 
  • Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNA(Phe) fr ...

    Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNA(Phe) from Escherichia coli at a resolution of 3 A. We show that in the absence of modifications the overall fold of the tRNA is essentially the same as that of mature tRNA. However, there are a number of significant structural differences, such as rearrangements in a triplet base pair and a widened angle between the acceptor and anticodon stems. Contrary to previous observations, the anticodon adopts the same conformation as seen in mature tRNA.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, North Yorkshire, YO10 5YW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Unmodified tRNAPheA76N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.226 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.450α = 90.00
b = 99.450β = 90.00
c = 110.330γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references