3TRA

RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 112-123

  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% fo ...

    Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% for about 4500 reflections between 10 and 3 A. In yeast tRNA(Asp) crystals the molecules exist as dimers with base pairings of the anticodon (AC) triplets and labilization of the tertiary interaction between one invariant guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine (T) loop (G19-C56). In yeast tRNA(Phe) crystals, the molecules exist as monomers with only weak intermolecular packing contacts between symmetry-related molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are identical when allowance is made for base sequence changes between tRNA(Phe) and tRNA(Asp). However, the relative mobilities of two regions are inverse in the two structures with the AC loop more mobile than the D loop in tRNA(Phe) and the D loop more mobile than the AC loop in tRNA(Asp). In addition, the T loop becomes mobile in tRNA(Asp). The present refinements were performed to exclude packing effects or refinement bias as possible sources of such differential dynamic behavior. It is concluded that the transfer of flexibility from the anticodon to the D- and T-loop region in tRNA(Asp) is not a crystal-line artefact. Further, analysis of the four structures supports a mechanism for the flexibility transfer through base stacking in the AC loop and concomitant variations in twist angles between base pairs of the anticodon helix which propagate up to the D- and T-loop region.


    Related Citations: 
    • Hydration of Transfer RNA Molecules. A Crystallographic Study
      Westhof, E., Dumas, P., Moras, D.
      (1988) Biochimie 70: 145
    • Three-Dimensional Structure of Yeast T-RNA-ASP. I. Structure Determination
      Comarmond, M.B., Giege, R., Thierry, J.C., Moras, D., Fischer, J.
      (1986) Acta Crystallogr B 42: 272
    • Anticodon-Anticodon Interaction Induces Conformational Changes in T-RNA. Yeast T-RNA-ASP, a Model for T-RNA-M-RNA Recognition
      Moras, D., Dock, A.-C., Dumas, P., Westhof, E., Romby, P., Ebel, J.-P., Giege, R.
      (1986) Proc Natl Acad Sci U S A 83: 932
    • Crystallographic Refinement of Yeast Aspartic Acid Transfer RNA
      Westhof, E., Dumas, P., Moras, D.
      (1985) J Mol Biol 184: 119
    • Crystal Structure of Yeast T-RNA-ASP. Atomic Coordinates
      Dumas, P., Ebel, J.P., Giege, R., Moras, D., Thierry, J.C., Westhof, E.
      (1985) Biochimie 67: 597
    • Loop Stereochemistry and Dynamics in Transfer RNA
      Westhof, E., Dumas, P., Moras, D.
      (1983) J Biomol Struct Dyn 1: 337
    • Crystal Structure of Yeast T-RNA-ASP
      Moras, D., Comarmond, M.B., Fischer, J., Weiss, R., Thierry, J.C., Ebel, J.P., Giege, R.
      (1980) Nature 288: 669
    • Yeast Transfer RNA-ASP. A New High-Resolution X-Ray Diffracting Crystal Form of a Transfer RNA
      Giege, R., Moras, D., Thierry, J.C.
      (1977) J Mol Biol 115: 91

    Organizational Affiliation

    Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
TRNAASPA75Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 3.00 Å
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.3α = 90
b = 68β = 90
c = 149.5γ = 90
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1987-11-06
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance