1EVV

CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 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

  • 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: 
    • 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.,Sect.A 44: 112
    • 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.USA 72: 4414


    Organizational Affiliation

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




Macromolecules

Find similar proteins 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 SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
A
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
A
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
A
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
A
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.252α = 90.00
b = 32.988β = 90.38
c = 61.882γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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