Abstract
The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals. The residuals from this comparison are low enough to conclude that at 4-Å resolution, the three-dimensional structure of the molecule in the monoclinic crystal is essentially the same as that in the orthorhombic crystal. In addition, a correlation coefficient calculated from intensities based on a skeletal model of the molecule also confirmed the structure in the monoclinic cell. Electron density difference maps, as well as the presence of close contacts in the anticodon loop region of the monoclinic crystal, suggest that the anticodon loop may have a slightly different conformation than that observed in the orthorhombic crystals.
Keywords: molecular replacement method, x-ray diffraction, orthorhombic tRNA crystal
Full text
PDF




Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Cramer F., von der Haar F., Holmes K. C., Saenger W., Schlimme E., Schulz G. E. Crystallization of yeast phenylalanine transfer ribonucleic acid. J Mol Biol. 1970 Aug;51(3):523–530. doi: 10.1016/0022-2836(70)90005-7. [DOI] [PubMed] [Google Scholar]
- Hackert M. L., Ford G. C., Rossmann M. G. Molecular orientation and position of the pig M4 and H4 isoenzymes of lactate dehydrogenase in their crystal cells. J Mol Biol. 1973 Aug 25;78(4):665–673. doi: 10.1016/0022-2836(73)90287-8. [DOI] [PubMed] [Google Scholar]
- Ichikawa T., Sundaralingam M. X-ray diffraction study of a new crystal form of yeast phenylalanine tRNA. Nat New Biol. 1972 Apr 12;236(67):174–175. doi: 10.1038/newbio236174a0. [DOI] [PubMed] [Google Scholar]
- Joynson M. A., North A. C., Sarma V. R., Dickerson R. E., Steinrauf L. K. Low-resolution studies on the relationship between the triclinic and tetragonal forms of lysozyme. J Mol Biol. 1970 May 28;50(1):137–142. doi: 10.1016/0022-2836(70)90110-5. [DOI] [PubMed] [Google Scholar]
- Kim S. H., Quigley G. J., Suddath F. L., McPherson A., Sneden D., Kim J. J., Weinzierl J., Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science. 1973 Jan 19;179(4070):285–288. doi: 10.1126/science.179.4070.285. [DOI] [PubMed] [Google Scholar]
- Kim S. H., Quigley G., Suddath F. L., McPherson A., Sneden D., Kim J. J., Weinzierl J., Rich A. Unit cell transormations in yeast phenylalanine transfer RNA crystals. J Mol Biol. 1973 Apr 5;75(2):429–432. doi: 10.1016/0022-2836(73)90032-6. [DOI] [PubMed] [Google Scholar]
- Kim S. H., Quigley G., Suddath F. L., McPherson A., Sneden D., Kim J. J., Weinzierl J., Rich A. X-ray crystallographic studies of polymorphic forms of yeast phenylalanine transfer RNA. J Mol Biol. 1973 Apr 5;75(2):421–428. doi: 10.1016/0022-2836(73)90031-4. [DOI] [PubMed] [Google Scholar]
- Ladner J. E., Finch J. T., Klug A., Clark B. F. High-resolution x-ray diffraction studies on a pure species of transfer RNA. J Mol Biol. 1972 Dec 14;72(1):99–101. doi: 10.1016/0022-2836(72)90071-x. [DOI] [PubMed] [Google Scholar]
- Levitt M. Orientation of double-helical segments in crystals of yeast phenylalanine transfer RNA. J Mol Biol. 1973 Oct 25;80(2):255–263. doi: 10.1016/0022-2836(73)90171-x. [DOI] [PubMed] [Google Scholar]
- Suddath F. L., Quigley G. J., McPherson A., Sneden D., Kim J. J., Kim S. H., Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution. Nature. 1974 Mar 1;248(5443):20–24. doi: 10.1038/248020a0. [DOI] [PubMed] [Google Scholar]