1TRA

RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 4868-4878

  • DOI: 10.1021/bi00365a022
  • Primary Citation of Related Structures:  
    1TRA

  • PubMed Abstract: 
  • The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times t ...

    The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times their standard deviations, the R factor is 16.8%. The variation of the atomic temperature factors along the sequence indicates that the major flexibility regions are the amino acid and anticodon stems. The two strands of the amino acid helix exhibit large differential temperature factors, suggesting partial uncoiling or melting of the helix. In this work, the occupancy of all atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well as U33 and G37 of the anticodon loop have occupancies around 70%, indicating some local disorder or large-scale mobility at these positions. One hundred fifteen solvent molecules, including five magnesium ions, were found in difference maps. The role of several water molecules is clearly related to the stabilization of the secondary and tertiary interactions. The gold sites, which were not previously discussed, are described and show an energetically favored binding mode similar to that of cobalt and nickel complexes with nucleotides.


    Related Citations: 
    • Crystal and Molecular Structure of Yeast Phenylalanyl Transfer RNA. Structure Determination, Difference Fourier Refinement, Molecular Conformation, Metal and Solvent Binding
      Stout, C.D., Mizuno, H., Rao, S.T., Swaminathan, P., Rubin, J., Brennan, T., Sundaralingam, M.
      (1978) Acta Crystallogr B 34: 1529
    • Atomic Coordinates and Molecular Conformation of Yeast Phenylalanyl T-RNA, an Independent Investigation
      Stout, C.D., Mizuno, H., Rubin, J., Brennan, T., Rao, S.T., Sundaralingam, M.
      (1976) Nucleic Acids Res 3: 1111
    • Mechanisms of Chain Folding in Nucleic Acids, the (Omega,Omega) Plot and Its Correlation to the Nucleotide Geometry in Yeast T-RNA(PHE)
      Sundaralingam, M., Mizuno, H., Stout, C.D., Rao, S.T., Liebman, M., Yathindra, N.
      (1976) Nucleic Acids Res 3: 2471
    • X-Ray Diffraction Study of a New Crystal Form of Yeast Phenylalanine T-RNA
      Ichikawa, T., Sundaralingam, M.
      (1972) Nature New Biol 236: 174

    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.



Macromolecules
Find similar nucleic acids by: 
(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: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56α = 90
b = 33.3β = 90.4
c = 63γ = 90
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-07-14
    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
  • Version 1.3: 2011-07-27
    Changes: Other