Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the <Emphasis Type="Italic">Thermophilic thermus</Emphasis> thermophilus strain HB27

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°С, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2₁ and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.     

Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium <Emphasis Type="Italic">Thermus thermophilus</Emphasis> strain HB27

Adenine phosphoribosyltransferase (APRT) belongs to the type I phosphoribosyltransferase family and catalyzes the formation of adenosine monophosphate via transfer of the 5-phosphoribosyl group from phosphoribosyl pyrophosphate to the nitrogen atom N9 of the adenine base. Proteins of this family are involved in a salvage pathway of nucleotide synthesis, thus providing purine base utilization and maintaining the optimal level of purine bases in the body. Adenine phosphoribosyltransferase from the extremely thermophilic Thermus thermophilus strain HB27 was produced using a highly efficient E. coli producer strain and was then purified by affinity and gel-filtration chromatography. This enzyme was successfully employed as a catalyst for the cascade biosynthesis of biologically important nucleotides. The screening of crystallization conditions for recombinant APRT from T. thermophilus HB27 was performed in order to determine the enzyme structure by X-ray diffraction. The crystallization conditions, which were found by the vapor-diffusion technique, were then optimized to apply the counter-diffusion technique. The crystals of the enzyme were grown by the capillary counter-diffusion method. The crystals belong to sp. gr. P12₁1 and have the following unitcell parameters: a = 69.86 Å, b = 82.16 Å, c = 91.39 Å, α = γ = 90°, β = 102.58°. The X-ray diffraction data set suitable for the determination of the APRT structure at 2.6 Å resolution was collected from the crystals at the SPring-8 synchrotron facility (Japan).     

Recombinant formate dehydrogenase from <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: Preparation,crystal growth in microgravity,and preliminary X-ray diffraction study

Crystals of high-purity recombinant NAD⁺-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul’-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 Å using an X-ray synchrotron source. The crystals belong to sp. gr. P4₃2₁2; the unit-cell parameters are a = b = 107.865 Å, c = 71.180 Å, α = β = γ = 90°.     

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from <Emphasis Type="Italic">Thermus Species</Emphasis> 2.9

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12₁1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.     

Preparation,crystallization, and preliminary X-ray diffraction study of mutant carboxypeptidase T containing the primary specificity pocket of carboxypeptidase B

Recombinant G215S, A251G, T257A, D260G, T262D mutant carboxypeptidase T from Thermoactinomyces vulgaris containing mutations in the primary specificity pocket was prepared and crystallized. Single crystals with a size of up to 0.3 mm were grown and investigated by X-ray diffraction. Recombinant mutant carboxypeptidase T containing the primary specificity subsite compositionally identical to that of pancreatic carboxypeptidase B crystallizes in the same space group as the natural enzyme. The crystals belong to sp. gr. P6₃22; the unit-cell parameters are a = b = 157.867 Å, c = 104.304 Å, α = β = 90°, γ = 120°. X-ray diffraction data suitable for determining the three-dimensional structure at atomic resolution were collected from one crystal.     

Disaccharide nucleosides: The crystal and molecular structure of 2′-<Emphasis Type="Italic">O</Emphasis>-β-<Emphasis Type="Italic">D</Emphasis>-ribopyranosylcytidine

The crystal structure of a disaccharide nucleoside, 2′-O-β-D-ribopyranosylcytidine, is studied using X-ray diffraction (space group P2₁, a = 6.827(2) Å, b = 12.813(3) Å, c = 9.532(2) Å, β = 92.934(5)°, V = 832.7(4) ų, Z = 2). The stereochemical features of the molecular structure of 2′-O-β-D-ribopyranosylcytidine are analyzed, and the structural data are compared with those obtained for the previously studied disaccharide nucleoside 2′-O-β-D-ribofuranosyluridine.     

Crystal structure and microtwinning of monoclinic La<Subscript>3</Subscript>SbZn<Subscript>3</Subscript>Ge<Subscript>2</Subscript>O<Subscript>14</Subscript> crystals of the langasite family

The crystal structure of monoclinic La₃SbZn₃Ge₂O₁₄ crystals from the langasite family is determined by X-ray diffraction analysis [a = 5.202(1) Å, b = 8.312(1) Å, c = 14.394(2) Å, β = 90.02(1)°, sp. gr. A2, Z = 2, and R/R _w = (5.2/4.6)%]. The structure is a derivative of the Ca₃Ga₂Ge₄O₁₄-type structure (a = 8.069 Å, c = 4.967 Å, sp. gr. P321, Z = 1). The crystal studied is a polysynthetic twin with the twin index n = 2, whose monoclinic components are related by pseudomerohedry by a threefold rotation axis of the supergroup P321.     

Structure of the homodimer of uridine phosphorylase from <Emphasis Type="Italic">Salmonella typhimurium</Emphasis> in the native state at 1.9 Å resolution

Uridine phosphorylase (UPh) belongs to pyrimidine nucleoside phosphorylases. This enzyme catalyzes cleavage of the C-N glycoside bond in uridine to form uracil and ribose-1’-phosphate. Uridine phosphorylase supplies cells with nucleotide precursors by catalyzing the phosphorolysis of purine and pyrimidine nucleosides. This is an alternative to de novo nucleotide synthesis. The three-dimensional structure of native uridine phosphorylase from Salmonella typhimurium (StUPh) in a new crystal form was solved and refined at 1.90 Å resolution (R _st = 20.37%; R _free = 24.69%; the rmsd of bond lengths and bond angles are 0.009 Å and 1.223°, respectively). A homodimer containing two asynchronously functioning active sites was demonstrated to be the minimum structural unit necessary for function of the hexameric StUPh molecule (L ₃3L ₂). Each active site is formed by amino acid residues of both subunits.     

Absolute structure of La<Subscript>3</Subscript>Ga<Subscript>5</Subscript>SiO<Subscript>14</Subscript> langasite crystals

The absolute structure of La₃Ga₅SiO₁₄ piezoelectric crystals (a = 8.1746(6) Å, c = 5.1022(4) Å, space group P321, Z = 1) with the positive sense of rotation of the plane of polarization is refined using X-ray diffraction analysis (R = 1.37%, R _w = 1.71%, 2413 unique reflections, max sinθ/λ = 1.15 Å^?1). The contributions from the anharmonicity of thermal vibrations of lanthanum atoms are calculated with the use of the components of the third-and fourth-rank tensors. It is demonstrated that these contributions can have a significant effect.     

Growth and crystal structure of binary molybdate CsFe(MoO<Subscript>4</Subscript>)<Subscript>2</Subscript>

CsFe(MoO₄)₂ single crystals have been grown by solution-melt crystallization with a charge-to-solvent ratio of 1: 3 (with Cs₂Mo₃O₁₀ used as a solvent). The crystal structure of this compound has been refined by X-ray diffraction (X8 APEX automatic diffractometer, MoK _α radiation, 356 F(hkl), R = 0.0178). The trigonal unit cell has the following parameters: a = b = 5.6051(2) Å, c = 8.0118(4) Å, V = 217.985(15) ų, Z = 1, ρ_calc = 3.875 g/cm³, and sp. gr. P \(\bar 3\) m1. The structure is composed of alternating layers of FeO₆ octahedra (with MoO₄ tetrahedra attached by sharing vertices) and CsO₁₂ icosahedra.     

Low-temperature X-ray diffraction studies of [(CH<Subscript>3</Subscript>)<Subscript>2</Subscript>NH<Subscript>2</Subscript>]<Subscript>5</Subscript>Cd<Subscript>3</Subscript>Cl<Subscript>11</Subscript> crystals

[(CH₃)₂NH₂]₅Cd₃Cl₁₁ crystals are grown by the method of isothermal evaporation from saturated aqueous solutions containing dimethylamine and cadmium chlorides, [(CH₃)2NH₂]Cl and CdCl_2.5H₂O. The crystal grown are studied by the X-ray diffraction method. It is established that the crystals are orthorhombic with the unit-cell parameters at room temperature a = 18.115 ± 0.004 Å, b = 11.432 ± 0.002 Å, and c = 15.821 ± 0.003 Å. The unit-cell parameters a, b, and c of the [(CH₃)₂NH₂]₅Cd₃Cl₁₁ crystals are measured as functions of temperature in the temperature range 100–320 K. The data obtained were used to determine the thermal expansion coefficients along the main crystallographic axes. The temperature curves of the unit-cell parameters and thermal expansion coefficients showed pronounced anomalies in the vicinity of the temperatures T ₁ = 120, T ₂ = 150, and T ₃ = 180 K corresponding to the phase transitions in the [(CH₃)₂NH₂]₅Cd₃Cl₁₁ crystals. The crystals are also characterized by a pronounced anisotropy of thermal expansion.     

Crystal structure of CoUO<Subscript>2</Subscript>(SO<Subscript>4</Subscript>)<Subscript>2</Subscript> · 5H<Subscript>2</Subscript>O at 293 K

Single crystals of cobalt uranyl sulfate are grown. The crystal structure is established by X-ray diffraction: the orthorhombic system, sp. gr. Pmc2₁, a = 6.452(2) Å, b = 8.295(2) Å, c = 11.288(3) Å, R₁ = 0.0303, wR₂ = 0.0735 for reflections with I > 2σ(I). The structure of CoUO₂(SO₄)₂ · 5H₂O consists of infinite two-dimensional uncharged [CoUO₂(SO₄)₂H₂O]_2∞ layers, which are linked to each other by hydrogen bonds.     

Crystal structure of the new radical cation salt (<Emphasis Type="Italic">DOET</Emphasis>)<Subscript>4</Subscript>[Fe(CN)<Subscript>5</Subscript>NO]<Subscript>1.25</Subscript>(C<Subscript>6</Subscript>H<Subscript>5</Subscript>Cl)<Subscript>0.75</Subscript>

A new radical cation salt based on 4,5-(1,4-dioxanediyl-2,3-dithio)-4′,5′-ethylenedithiotetrathiafulvalene (DOET) with the photochromic anion [Fe(CN)₅NO]^2?, namely, (DOET)₄[Fe(CN)₅ NO]_1.25(C₆H₅Cl)_0.75, is synthesized. Single crystals of this salt are studied using X-ray diffraction [a = 10.398(2) Å, b = 11.168(2) Å, c = 18.499(4) Å, α = 103.14(3)°, β = 92.80(3)°, γ = 106.02(3)°, V = 1996.3(7) ų, space group \(P\bar 1\), and Z = 1]. In the structure, radical cation layers alternate with anion layers along the c axis. The centrosymmetric dimers are formed by DOET radical cations in the donor layer with packing of the β type. Like the vast majority of DOET-based salts, the new salt possesses semiconductor properties.     

Crystal structure of the Ca<Subscript>3</Subscript>TaGa<Subscript>3</Subscript>Si<Subscript>2</Subscript>O<Subscript>14</Subscript> compound

The absolute crystal structure of the Ca₃TaGa₃Si₂O₁₄ piezoelectric compound is refined using X-ray diffraction analysis. The unit cell parameters and final R factors are as follows: a = 8.112(1) Å, c = 4.9862(6) Å, space group P321, Z = 1, R = 0.98%, and R _w = 1.42%. It is shown that the configuration of the absolute crystal structure inherited from the seed material determines the positive sense of the optical activity of the crystal under investigation. The structural and acoustical characteristics of the Ca₃TaGa₃Si₂O₁₄ crystals are compared with those of the La₃Ga₅SiO₁₄ crystals.     

Crystal structure and spectral characteristics of 2,4,7-trinitro-9-fluorenone

The crystal structure of 2,4,7-trinitro-9-fluorenone C₁₃H₅N₃O₇ is determined by X-ray diffraction analysis. The crystals are monoclinic, a = 4.024(1) Å, b = 16.763(3) Å, c = 18.250(4) Å, β = 96.32(3)°, V = 1223.6(5) ų, Z = 4, space group P2₁/c, and R = 0.0640 for 605 reflections with I > 2σ(I). The crystal is built of planar isolated molecules. The compound is characterized using IR and electronic absorption spectroscopy.     

X-ray diffraction study of thiocarbamide hydrochloride

Thiocarbamide hydrochloride single crystals forming a salt with the composition [(NH₂)₂CSH]⁺Cl^? are studied by the X-ray diffraction method. The tetragonal crystals have the unit-cell parameters a = 7.556(1) Å and c = 18.329(3) Å, V = 1046.5 ų, Z = 8, ρ_calcd = 1.436 g/cm³, sp. gr. P4₁2₁2, and R = 0.050. Each chloride anion in the crystal forms five hydrogen bonds with thee different cations.     

Synthesis and structure of methyl 8-allyl-6-bromo-2-methyl-1,2,3,4-tetrahydroquinoline-4-carboxylate

The compound C₁₅H₁₈NO₂Br was synthesized and characterized by X-ray diffraction. The crystals belong to the monoclinic system, sp. gr. P2₁/n, a = 8.913(2) Å, b = 23.637(6) Å, c = 13.892(3) Å, β = 90.31(2)°, Z = 8, V = 2926.8(12) ų, ρ_calc = 1.472 g/cm³. The bond lengths and bond angles in two molecules are equal within an experimental error and are typical of this class of compounds. The conformational differences of the saturated heterocyclic and methoxycarbonyl fragments of the molecules result in the presence of two crystallographically independent molecules in the crystal structure.     

X-ray mapping in heterocyclic design: XV. Tricyclic heterocycles based on 2-oxo-2,5,6,7-tetrahydro-1<Emphasis Type="Italic">H</Emphasis>-cyclopenta[<Emphasis Type="Italic">b</Emphasis>]pyridine-3-carbonitrile

The structures of five compounds are studied using single-crystal X-ray diffraction: 2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 15.641(8) Å, b = 9.373(5) Å, c = 7.387(4) Å, β = 92.91(5)°, Z = 4, space group P2₁/c]; 1-[2-(4-chlorophenyl)-2-oxoethyl]-2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 4.728(4) Å, b = 28.035(11) Å, c = 11.184(3) Å, Z = 4, space group P2₁2₁2₁]; 2-[2-(4-chlorophenyl)-2-oxoethoxy]-6,7-dihydro-5H-cyclopenta[b]pyridine-3-carbonitrile [a = 10.1202(13) Å, b = 11.2484(18) Å, c = 13.4323(19) Å, β = 102.05(1)°, Z = 4, space group P2₁/c]; 2-(4-chlorophenyl)-3a, 6,7,8-tetrahydrocyclopenta[e][1.3]oxazolo[3.2-a]pyridine-4-carboxamide perchlorate [a = 7.702(2) Å, b = 9.599(3) Å, c = 23.798(5) Å, β = 93.44(2)°, Z = 4, space group P2₁/c]; and (3-amino-6,7-dihydro-5H-cyclopenta[b]furo[3.2-e]pyridin-2-yl)(4-chlorophenyl)methanone [a = 7.3273(2) Å, b = 13.390(3) Å, c = 28.792(8) Å, Z = 8, space group Pbca]. The structures are solved using direct methods and refined by the full-matrix least-squares procedure in the anisotropic approximation to R = 0.0580, 0.0724, 0.0469, 0.0477, and 0.0418, respectively.     

X-ray mapping in heterocyclic design: 16. X-ray diffraction study of 1-(4-chlorophenacyl)-4-methyl-1,5,6,7-tetrahydro-2<Emphasis Type="Italic">H</Emphasis>-cyclopenta[<Emphasis Type="Italic">b</Emphasis>]pyridin-2-one

The structure of 1-(4-chlorophenacyl)-4-methyl-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one is studied using single-crystal X-ray diffraction. The structure (a = 37.006(8) Å, b = 8.967(3) Å, c = 27.911(3) Å, β = 96.52(2)°, Z = 24, space group P2₁/c) is solved by direct methods and refined to R₁ = 0.0608 and wR₂ = 0.1170. Six crystallographically independent molecules differ in the dihedral angle between the phenyl and heterocycle planes. The formation of Cl?Cl aggregates is discussed.     

New multicell model for describing the atomic structure of La<Subscript>3</Subscript>Ga<Subscript>5</Subscript>SiO<Subscript>14</Subscript> piezoelectric crystal: Unit cells of different compositions in the same single crystal

Accurate X-ray diffraction study of langasite (La₃Ga₅SiO₁₄) single crystal has been performed using the data obtained on a diffractometer equipped with a CCD area detector at 295 and 90.5 K. Within the known La₃Ga₅SiO₁₄ model, Ga and Si cations jointly occupy the 2d site. A new model of a “multicell” consisting of two different unit cells is proposed. Gallium atoms occupy the 2d site in one of these cells, and silicon atoms occupy this site in the other cell; all other atoms correspondingly coordinate these cations. This structure implements various physical properties exhibited by langasite family crystals. The conclusions are based on processing four data sets obtained with a high resolution (sin θ/λ ≤ 1.35 Å^–1), the results reproduced in repeated experiments, and the high relative precision of the study (sp. gr. P321, Z = 1; at 295 K, a = 8.1652(6) Å, c = 5.0958(5) Å, R/wR = 0.68/0.68%, 3927 independent reflections; at 90.5 K, a = 8.1559(4) Å, c = 5.0913(6) Å, R/wR = 0.92/0.93%, 3928 reflections).