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 Å

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


  • 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.,Sect.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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
TRNAPHEA76Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 3 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.000α = 90.00
b = 33.300β = 90.40
c = 63.000γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-07-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-07-27
    Type: Other