1EVV

CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.

Jovine, L., Djordjevic, S., Rhodes, D.

(2000) J Mol Biol 301: 401-414

  • DOI: 10.1006/jmbi.2000.3950
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previo ...

    We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+).

    Related Citations: 
    • High-resolution X-ray diffraction studies on a pure species of transfer RNA
      Ladner, J.E., Finch, J.T., Klug, A., Clark, B.F.
      (1972) J Mol Biol 72: 99
    • Structure of yeast phenylalanine tRNA at 3 A resolution
      Robertus, J.D., Ladner, J.E., Finch, J.T., Rhodes, D., Brown, R.S., Clark, B.F.C., Klug, A.
      (1974) Nature 250: 546
    • Structure of yeast phenylalanine transfer RNA at 2.5 A resolution
      Ladner, J.E., Jack, A., Robertus, J.D., Brown, R.S., Rhodes, D., Clark, B.F., Klug, A.
      (1975) Proc Natl Acad Sci U S A 72: 4414
    • Further refinement of the structure of yeast tRNA Phe
      Hingerty, B., Brown, R.S., Jack, A.
      (1978) J Mol Biol 124: 523
    • Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
      Westhof, E., Sundaralingam, M.
      (1986) Biochemistry 25: 4868
    • Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
      Westhof, E., Dumas, P., Moras, D.
      (1988) Acta Crystallogr A 44: 112
    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.



Macromolecules

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
PHENYLALANINE TRANSFER RNAA76Saccharomyces
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.252α = 90
b = 32.988β = 90.38
c = 61.882γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance