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S V Pletnev

Publications and source records attributed to S V Pletnev.

5 recordsLinked to original sources
PubMed2001

Combining electron microscopic with x-ray crystallographic structures.

Analgorithm has been developed for placing three-dimensional atomic structures into appropriately scaled cryoelectron microscopy maps. The first stage in this process is to conduct a three-dimensional angular search in which the center of gravity of an X-ray crystallographically determined structure is placed on a selected position in the cryoelectron microscopy map. The quality of the fit is measured by the sum of the density at each atomic position. The second stage is to refine the three angles and three translational parameters for the best (usually 25 to 100) fits. Useful criteria for this refinement include the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure. These refinements generally lead to a convergence of the originally chosen, top scoring fits to just a few (about 3 to 8) acceptable possibilities. Usually, the best remaining fit is clearly superior to any of the others.

Cryoelectron Microscopy↗
PubMed1997

The crystal and molecular structure of a valinomycin analogue cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)]. H2O(C50H82N6 O18.H2O).

The crystal and molecular structure of the valinomycin analogue, cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)] has been solved by x-ray direct methods using the "Shake and Bake" procedure. The crystals, grown from a mixture of octane/CH2Cl2, belong to space group P2(1) (Z = 4) with cell parameters a = 10.29, b = 32.08, c = 18.73 A, beta = 97.05 degrees, and contain two molecules per asymmetric unit. After anisotropic refinement the standard reliability factor was Rl = 0.058. The conformations of both independent molecules is similar to that observed for isoleucinomycin, cyclo[-(D-Ile-L-Lac-L-Ile-D-Hyi)3] [V. Z. Pletnev et al. (1980) Biopolymers, Vol. 19, pp. 1517-1534]. The structure has an asymmetric conformation stabilized by six intramolecular H bonds, five bonds being of the 4-->1 type and one bond being of the 5-->1 type. One water molecule is caged in the internal cavity of each cyclodepsipeptide. This conformation could represent an intermediate state between free and complexed forms of valinomycin.

Crystallography, X-Ray↗
PubMed1996

Purification and crystals of tyrosine phenol-lyase from Erwinia herbicola.

New method of purification of tyrosine phenol-lyase from Erwinia herbicola has been developed. The enzyme obtained is homogeneous and characterised by a specific activity which is three times higher then that described earlier. Crystals of holoenzyme complexed with monovalent cations have been grown from NaCl, KCl and (NH4)2SO4 containing solutions. The crystals belong to P6(2)22 space group. They are stable to the X-ray radiation and diffract up to 2.6-3.1 A. Asymmetric unit contains one subunit of tetrameric molecule.

Crystallization↗
PubMed1995

Crystal and molecular structure of the centrosymmetric meso-valinomycin analogue--cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi-L-Val-D-Hyi-D-Val-L-Hy i) (C60H102N6O18).

The crystal structure of cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi -L-Val-D-Hyi-D-Val-L-Hyi).2H2O has been solved by x-ray direct methods. The crystals (grown from a mixture of octane/CH2Cl2) are an orthorhombic, centrosymmetric space group Pbca, cell parameters a = 11.458 (2), b = 25.613 (3), c = 23.691 (3) A, Z = 4; therefore the molecule lies on a center of inversion in the cell. The atomic coordinates for the C, N, and O atoms were refined in the anisotropic thermal motion approximation (allowing for H-atom contribution to Fcal) to a standard R-factor value of 0.081. In contrast to meso-valinomycin, the analogue under study does not adopt an octahedral cage bracelet conformation. It has an unusual centrosymmetric elongated form with two type II terminal beta-bends formed by N-H ... C=O 4-->1 type intramolecular H bonds. Two symmetry-related water molecules reside in the elongated molecular cavity of the centrosymmetric depsipeptide ring.

Crystallization↗