4TRA

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: 0.172 

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

  • Primary Citation of Related Structures:  
    3TRA, 4TRA, 2TRA

  • 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
    • Crystal Structure of Yeast Phenylalanine T-RNA. I.Crystallographic Refinement
      Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M., Kim, S.-H.
      (1978) J Mol Biol 123: 607
    • Crystal Structure of Yeast Phenylalanine T-RNA. II.Structural Features and Functional Implications
      Holbrook, S.R., Sussman, J.L., Warrant, R.W., Kim, S.-H.
      (1978) J Mol Biol 123: 631
    • Three Dimensional Structure of T-RNA and its Functional Implications
      Kim, S.-H.
      (1978) Adv Enzymol Relat Subj Biochem 46: 279
    • The Three-Dimensional Structure of Transfer RNA
      Rich, A., Kim, S.H.
      (1978) Sci Am 238: 52
    • Crystal Structure of Yeast Phenylalanine T-RNA, its Correlation to the Solution Structure and the Functional Implications
      Kim, S.-H.
      (1978) Transfer Rna --: --
    • RNA-Ligand Interactions. (1) Magnesium Binding Sites in Yeast T-RNA-PHE
      Holbrook, S.R., Sussman, J.L., Warrant, R.W., Church, G.M., Kim, S.-H.
      (1977) Nucleic Acids Res 4: 2811
    • Idealized Atomic Coordinates of Yeast Phenylalanine Transfer RNA
      Sussman, J.L., Kim, S.-H.
      (1976) Biochem Biophys Res Commun 68: 89
    • Three-dimensional Structure of a Transfer RNA in Two Crystal Forms
      Sussman, J.L., Kim, S.-H.
      (1976) Science 192: 853

    Organizational Affiliation

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
TRNAPHEA76Saccharomyces 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: 0.172 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33α = 90
b = 56β = 90
c = 161γ = 90
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report



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: Non-polymer description, Version format compliance