1TRA

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

Replaces:  8TNAReplaces:  2TNAReplaces:  7TNA

Summary for 1TRA

• Entry DOI: 10.2210/pdb1tra/pdb
• Descriptor: TRNAPHE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: t-rna, single strand, loops
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 25011.65

Authors

Westhof, E.,Sundaralingam, M. (deposition date: 1986-05-16, release date: 1986-07-14, Last modification date: 2024-02-14)

Primary citation

Westhof, E.,Sundaralingam, M.
Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.
Biochemistry, 25:4868-4878, 1986

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 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.

PubMed: 3533142
DOI: 10.1021/bi00365a022

Experimental method

X-RAY DIFFRACTION (3 Å)