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).     

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.     

Electron diffraction study of 1<Emphasis Type="Italic">M</Emphasis> illites with interstratified <Emphasis Type="Italic">trans</Emphasis>- and <Emphasis Type="Italic">cis</Emphasis>-vacant 2 : 1 layers

Illites from the volcanogenic Zn-Au-Ag sulfide deposit Galkinskoe (Northern Urals) have been investigated using oblique-texture electron diffraction patterns in combination with the simulation of diffraction effects. Along with single-phase tv/cv1M illites, the structures of which are formed by statistically interstratified dioctahedral 2: 1 layers with vacant trans- or cis-octahedra, illites in the form of a mixture of two interstratified tv/cv1M phases, with the dominance of tv- or cv layers, are identified. It is shown that in the latter case the diffraction pattern can also be interpreted within the single-phase tv/cv model, provided that the tv- and cv layers are distributed with some tendency to segregate. The structural features indicating the preference of the two-phase model are analyzed.     

A New <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethyl Purine from an Australian <Emphasis Type="Italic">Dictyoceratid Sponge</Emphasis>

Abstract  

N6-methyl mucronatine (C₈H₁₂N₅O) has been isolated from a dictyoceratid sponge collected in South East Queensland. The solid state structure of the new metabolite (I) was confirmed by X-ray crystallography, while an NMR study in d ₄-MeOH reveals the presence of a minor tautomer identified as (II).     

X-ray analysis of sideroxol from <Emphasis Type="Italic">Sideritis leptoclada</Emphasis>

Sideroxol (1), a kaurane diterpene which has the ent-7α,18-dihydroxy-15β,16β-epoxykaurane structure (MW = 320.47, C₂₀H₃₂O₃) was obtained from the acetone extract of Sideritis leptoclada plant as well as from some other Sideritis species. It crystallizes in the orthorhombic space group P2₁, 2₁, 2₁ with a = 10.967(3), b = 24.555(5), c = 6.372(4) Å, Dc = 1.240 g cm⁻³, Z = 4, and refines to R = 0.065 for 721 independent reflections. The skeleton consists of three fused six-membered rings and a five-membered ring with fused epoxide. The six membered rings exhibited slightly distorted chair conformation. In addition to sideroxol, two kaurane and five kaurene diterpenes were isolated from the hexane and acetone extracts of the studied plant.     

Crystallization and Preliminary X-ray Diffraction Study of Purine Nucleoside Phosphorylase from the Thermophilic Bacterium <Emphasis Type="Italic">Thermus thermophilus</Emphasis> Strain HB27

Recombinant purine nucleoside phosphorylase from the thermophilic Thermus thermophilus strain encoded by the TT_C0194 gene was purified to homogeneity. The crystallization conditions for the enzyme were found by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown under microgravity conditions by the capillary counter-diffusion method. The crystals belong to sp. gr. P2₁2₁2₁ and have the following unit-cell parameters: a = 89.9 Å, b = 121.0 Å, c = 215.7 Å, α = β = γ = 90°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure of purine nucleoside phosphorylase was collected from the grown crystals at the SPring-8 synchrotron facility to 2.5 Å resolution.     

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°.     

Comparative analysis of spatial organization of laccases from <Emphasis Type="Italic">Cerrena maxima</Emphasis> and <Emphasis Type="Italic">Coriolus zonatus</Emphasis>

Laccase (oxygen oxidoreductase, EC 1.10.3.2) belongs to the multicopper oxidase family. The main function of this enzyme is to perform electron transfer from the oxidized substrate through the mononuclear copper-containing site T1 to the oxygen molecule bound to the site T3 in the trinuclear T2/T3 cluster. The structures of two new fungal laccases from C. maxima and C. zonatus were solved on the basis of synchrotron X-ray diffraction data. Both laccases show high structural homology with laccases from other sources. The role of the carbohydrate component of laccases in structure stabilization and formation of ordered protein crystals was demonstrated. In the structures of C. maxima and C. zonatus laccases, two water channels of functional importance were found and characterized. The structural results reported in the present study characterize one of the functional states of the enzyme fixed in the crystal structure.     

Crystal Structure of Two <Emphasis Type="Italic">V</Emphasis>-shaped Ligands with <Emphasis Type="Italic">N</Emphasis>-Heterocycles

Two V-shaped ligands with N-heterocycles, bis(4-(1H-imidazol-1-yl) phenyl)methanone (1), and bis(4-(1H-benzo[d]imidazol-1-yl)phenyl)methanone (2) have been synthesized and characterized by elemental analyses, IR and 1H NMR spectroscopy. Crystal structures of 1 and 2 have been determined by X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. P2₁/c, Z = 4. The crystal of 2 is orthorhombic, sp. gr. Fdd2, Z = 8. X-ray diffraction analyses show that the V-shaped angles of 1 and 2 are 122.72(15)° and 120.7(4)°, respectively. Intermolecular C–H···O, C–H···N, C–H···π, and π···π interactions link the components into three-dimensional networks in the crystal structures.     

Electron diffraction study of lizardite 1<Emphasis Type="Italic">T</Emphasis> with stacking faults

The stacking faults observed in the structure of the mineral lizardite 1T belonging to the polytype group A are investigated using the digital oblique-texture electron diffraction patterns, difference Fourier-potential maps, and model diffraction patterns obtained for this compound. Numerical simulation of the diffraction profiles along the first (the 02l and 11l reflections) and second (the 20l and 13l reflections) ellipses in the oblique-texture electron diffraction patterns is performed for finite sequences of ten layers with the use of the Markovian statistical model in the quasi-homogeneous approximation. The specific features of the intensity distributions along the first and second ellipses are associated with the manifestation of translational (displacements of the layers by ±b/3) and orientational (rotations of the layers through an angle of 180°) defects of the layer stacking, respectively. For both ellipses, the experimentally observed intensity distributions are in the best agreement with the diffraction profiles calculated for stacking faults at a content of approximately 25%, the short-range order parameter S = 1, and the maximum degree of ordering in the layer alternation. It is demonstrated that the irregularities revealed in the layer alternation in the structure of lizardite 1T (which is characterized by an identical orientation of the adjacent layers) arise from layer displacements by ±b/3 and, to a considerable extent, from the formation of sequences with opposite orientations of the adjacent layers. As a result, the structure of lizardite 1T nanocrystals involves a combination of layer sequences that are typical of structures belonging to the polytype groups A and D.     

Structure of 6,13-bis(<Emphasis Type="Italic">N</Emphasis>, <Emphasis Type="Italic">N</Emphasis>-dimethylcarbamoyl) thioquinanthrene

The crystal structure of 6,13-bis-(N,N-dimethylcarbamoyl)thioquinanthrene 3 has been determined as monoclinic, with space group P2(1)/c with lattice parameters a = 10.044(2) Å, b = 21.385(4) Å, c = 10.889(3) Å, = 102.92(3)°, Z = 4 and D_calc = 1.342 Mg/m³. The middle 1,4-dithiin ring in the title compound 3, C₂₄H₂₀N₄O₂S₂ is in a boat conformation with the dihedral angle between the planes of the aromatic rings 132.45(8)°.     

Structure of Triammonium <Emphasis Type="Italic">fac</Emphasis>-Trichloridotrioxidorhenate(VII) Chloride with <Emphasis Type="Italic">C</Emphasis><Subscript>3<Emphasis Type="Italic">v</Emphasis></Subscript> Crystallographic Symmetry of the Complex Anion

Abstract  

The unstable crystals of triammonium fac-trichloridotrioxidorhenate(VII) chloride have been obtained from ammonium rhenate(VII) solution in concentrated hydrochloric acid. The crystal structure consists of fac-trichloridotrioxidorhenate(VII) anions, chloride anions and ammonium cations. Each fac-trichloridotrioxidorhenate(VII) anion and each chloride anion lies in special position of 3m site symmetry (cell parameters: a = 9.026(3) Å; c = 7.690(4) Å; space group: P6₃ mc). The ammonium cation lies in special position of m site symmetry. The following anion geometrical parameters of the fac-trichloridotrioxidorhenate(VII) anion have been obtained: Re–O bond length of 1.720(2) Å, Re–Cl bond length of 2.5428(9) Å, the bond angles: O–Re–O of 103.5(1)° and Cl–Re–Cl of 79.8(1)°.     

Synthesis,redox properties,and X-ray diffraction structure of 2,3-<Emphasis Type="Italic">bis</Emphasis>(ethylthio)-<Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">p</Emphasis>-MeOC<Subscript>6</Subscript>H<Subscript>4</Subscript>)maleimide

Refluxing 2,3-dichloromaleic anhydride with p-anisidine in benzene with water removal gives the condensation product 2,3-dichloro-N-(p-MeOC₆H₄)maleimide (1) 75% yield. This new maleimide compound reacts with added ethanethiol in the presence of Et₃N or DBU to furnish the bidentate sulfide ligand 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) in 85% yield. Each product has been characterized in solution by IR, NMR, and UV-vis spectroscopies, and the solid-state structure of 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide was unequivocally established by single-crystal X-ray diffraction analysis. 2,3-bis(Ethylthio)-N-(p-MeOC₆H₄)maleimide crystallizes in the monoclinic space group C2/c, a = 20.035(3)Å, b = 9.188(1)Å, c = 16.887(2)Å, = 93.696(2)°, V = 3102.3(8)ų, Z = 8, and D_calcd = 1.385 mg/m³; R = 0.0268, R_w = 0.0676 for 2025 reflections with I > 2 (I). The nature of the LUMO in 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) has been determined by extended Hückel molecular orbital calculations, and these data are discussed relative to the cyclic voltammetry results and other structurally relevant compounds prepared in our labs.     

Crystal and Molecular Structures of Di-1-Adamantylthiophosphinic Chloride, <Emphasis Type="Italic">P</Emphasis>,<Emphasis Type="Italic">P</Emphasis>-Diphenyl-<Emphasis Type="Italic">N</Emphasis>-Benzyl Phosphinothioic- and Selenoic- Amides

Abstract  Synthesis and X-ray structural determination of three phosphorus compounds are reported. (3b) is monoclinic P2(1)/c with a = 11.852(1), b = 12.825(1), c = 12.445(1) ?, β = 103.693(1)o; (4a) and (4b) are monoclinic P2(1)/n with a = 12.1422(16), b = 9.0860(12), c = 14.845(2) ?, β = 96.498(3)o for (4a), and a = 12.2714(16), b = 9.2812(12), c = 14.800(2) ?, β = 97.176(2)o for (4b). They all exhibit distorted tetrahedral geometry about the P atom. Ph₂P(X)NHC₇H₇ (X=S (4a) and X=Se (4b)) show typical P–S and P–Se double bond distances and P–N single bonds, while P–S bond in 1-Ad₂P(S)Cl (3b) is comparable to P–S single bonded probably due to the largeness of 1-adamantyl groups. Graphical Abstract  Synthesis and X-ray structural determination of 1-Ad₂P(S)Cl (3b), Ph₂P(S)NHC₇H₇ (4a) and Ph₂P(Se)NHC₇H₇ (4b) are reported.      

Structural Features of <Emphasis Type="Italic">Ortho</Emphasis>-hydroxy Bis-phenols and Their Comparison with <Emphasis Type="Italic">Para</Emphasis>-hydroxy Bis-phenols

Abstract The crystal structures of four bis-phenols are reported to substantiate the fact that the weak interactions play a major role in the crystal packing of bis-phenols. The reaction of 2,4-dimethylphenol with aldehydes such as 2-naphthaldehyde, terephthaldehyde in the presence of trifluoracetic acid gave 2-[bis(2-hydroxy 3,5-dimethylphenyl)methyl]naphthalene (1) and 4-[bis(2-hydroxy 3,5-dimethylphenyl) methyl]benzaldehyde (2), respectively. The 2-[bis-(2-hydroxy 3,5-dimethylphenyl)-methyl]naphthalene (1) crystallizes in orthorhombic, Pbca, a = 11.905(3) ?, b = 18.788(5) ?, c = 18.894(5) ?, 4-[bis(2-hydroxy 3,5-dimethylphenyl)methyl] benzaldehyde (2) in monoclinic, Cc, a = 8.880(3) ?, b = 16.394(7) ?, c = 13.700(5) ?, γ = 104.542(2)°. The reaction of 2-nitrobenzaldehyde with 2,4-dimethylphenol gave 2-benzo[c] isoxazo-3-yl 4,6-dimethylphenol (3) and its crystal parameters are orthorhombic, P2₁2₁2₁, a = 7.737(6) ?, b = 11.885(9) ?, c = 13.336(8) ?. The reaction of 2,6-dimethylphenol with 4-nitrobenzaldehyde and 2-chlorobenzaldehyde gave bis(4-hydroxy 3,5-dimethylphenyl)(4-nitrophenyl)methane (4) and bis(4-hydroxy 3,5-dimethylphenyl)(2-chlorophenyl)methane (5), respectively. The bis(4-hydroxy 3,5dimethylphenyl)(4-nitrophenyl)methane (4) crystallizes in monoclinic, C2/c, a = 25.921(1) ?, b = 12.202(4) ?, c = 15.6084(7) ?, β = 122.172(4)°, and bis(4-hydroxy 3,5-dimethylphenyl) (2-chlorophenyl)methane crystallizes as acetonitrile solvate (5) in triclinic, P-1, a = 12.314(3) ?, b = 14.111(3) ?, c = 15.078(5) ?, α = 98.268(2)°, β = 111.268(2)°, γ = 114.304(1)˚. The unit cell of 5 contains two pairs of crystallographically unsymmetric molecules of bis-phenols. Index abstract The crystal structures of four bis-phenols are reported to substantiate the fact that the weak interactions plays a major role in crystal packing and can induce symmetry non-equivalence among bis-phenols in unit cell of bis-phenols.      

Structure of octaheme cytochrome <Emphasis Type="Italic">c</Emphasis> nitrite reductase from <Emphasis Type="Italic">Thioalkalivibrio nitratireducens</Emphasis> in a complex with phosphate

Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of the oxidized complex of TvNiR with phosphate and of this complex reduced by europium(II) chloride (1.8- and 2.0-Å resolution, the R factors are 15.9 and 16.7%, respectively) and the structure of the enzyme in the complex with cyanide (1.76-Å resolution, the R factor is 16.5%), which was prepared by soaking a crystal of the oxidized phosphate complex of TvNiR. In the active site of the enzyme, the phosphate ion binds to the iron ion of the catalytic heme and to the side chains of the catalytic residues Arg131, Tyr303, and His361. The cyanide ion is coordinated to the heme-iron ion and is hydrogen bonded to the residue His361. In the structure of reduced TvNiR, the phosphate ion is bound in the same manner as in the structure of oxidized TvNiR, and the nine_coordinated europium ion is located on the surface of one of the crystallographically independent monomers of the enzyme.     

2<Emphasis Type="Italic">D</Emphasis> quasi-periodic Rauzy tiling as a section of 3<Emphasis Type="Italic">D</Emphasis> periodic tiling

A method for constructing a 2D quasi-periodic Rauzy tiling Til as a section of some 3D periodic tiling Til ^3D is considered. The translation lattice of the tiling Til ^3D and its connectivity graph are constructed using the discrete modeling of packings. The calculation of the layer-by-layer growth polyhedron for the tiling Til ^3D made it possible to estimate from upper the shape of a growth polygon for the tiling Til. As a result, the growth shape in six out of eight growth sectors has been rigorously proven. A set of quasi-periodic tilings (locally indistinguishable from the Rauzy tiling Til), including seven centrosymmetric tilings, has been obtained.     

Synthesis and structural studies of <Emphasis Type="Italic">tris</Emphasis>-2-chlorobenzylamine and <Emphasis Type="Italic">tris</Emphasis>-2-bromobenzylamine

The tris-2-chloro and 2-bromotribenzylamines are prepared from aqueous ammonia and 2-chlorobenzyl chloride and 2-bromobenzyl bromide, respectively, in ethanol. Recrystallization yielded colorless cubes of each product. The crystal structures are each solved in space group P , and are isostructural. The tris-2-chloro compound, 1, has a = 7.4226(5) Å, b = 9.0825(7) Å, c = 14.529(1) Å, = 78.279(1), = 82.389(1), = 84.661(1), and V = 948.41(12) ų with Z = 2, and d_calc = 1.368 Mg/m³. The tris-2-bromo analog, 2, has a = 7.6569(11) Å, b = 9.0922(13) Å, c = 14.614(2) Å, = 79.286(2), = 81.777(2), = 85.401(2), and V = 987.9(2) ų with Z = 2, and d_calc = 1.762 Mg/m³. Lithium–halogen exchange experiments conducted in tetrahydrofuran at –78C using n-butyl lithium revealed that no exchange occurred for the tris-2-chloro compound, but did occur for the tris-2-bromo analog to yield tribenzylamine upon quench and work-up.     

Purification,isolation, crystallization,and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P322₁. The structure was solved by the molecular replacement method. The structure refinement is currently underway.