Crystallization and Preliminary X-Ray Analysis of Thermoactinomyces vulgaris R-47 α-Amylase II

Crystals of Thermoactinomyces vulgaris α-amylase II, which is a new type of α-amylase having hydrolysis activities for pullulan and cyclodextrins, have been obtained and diffraction data to 2.9 Å resolution were collected. The crystal belongs to an orthorhombic system with cell dimensions of a = 119.5 Å, b = 120.6 Å, and c = 114.6 Å and a space group of P 2₁2₁2₁. Two or three protein molecules are expected to exist in an asymmetric unit.     

Crystallization and Preliminary X-Ray Analysis of Neuropsin, a Serine Protease Expressed in the Limbic System of Mouse Brain

Neuropsin (M_r25 032) is a serine protease expressed in the limbic system of mouse brain. It has been implicated in various neurological processes including formation of memory and may be important as a drug target in the treatment of epilepsy. The recombinant protein was produced using a baculovirus expression system and was purified. Two crystal forms were obtained by a hanging-drop vapor-diffusion method with polyethylene glycol. Preliminary X-ray crystallographic analysis revealed that crystal form I belongs to triclinic space groupP1 with unit cell dimensionsa= 97.16 Å,b= 97.12 Å,c= 46.75 Å and α = 99.17°, β = 99.77°, γ = 117.35°. Self-rotation function analysis of these data of form I indicates the position of a noncrystallographic threefold axis. There are six molecules in the crystallographic asymmetric unit. Crystal form II also belongs to triclinic space groupP1 but has unit cell dimensions ofa= 38.40 Å,b= 55.16 Å,c= 65.37 Å and α = 95.38°, β = 89.98°, γ = 110.46° with two molecules in the crystallographic asymmetric unit. Form II has a noncrystallographic twofold axis. Intensity data to 3.1 Å resolution for form I and to 2.2 Å resolution for form II have been collected.     

New Crystal Forms of the Motile Major Sperm Protein (MSP) ofAscaris suum

We have obtained two new crystal forms of theAscarismajor sperm protein (MSP) that mediates amoeboid cell motility in nematode sperm. We obtained crystals with C2 symmetry from bacterially expressed α-MSP witha= 216.5 Å,b= 38.6 Å,c= 32.5 Å, γ = 93.1° and also crystals with P2₁symmetry from native β-MSP witha= 63.1 Å,b= 91.7 Å,c= 72.5 Å, γ = 91.3°. A full native data set has been collected for each crystal form using synchrotron radiation. Both crystal forms diffract to 2 Å and are suitable for high-resolution structural investigation.     

Heterocyclic compounds containing antimony 1. Synthesis, physicochemical properties, crystal and molecular structure of 2-(β-hydroxyethylthio) 1,3,2-oxathiastibolane

The compound (HOCH₂CH₂S) ) (1) has been prepared by the reaction of antimony(III) isopropoxide and 2-mercaptoethanol in a 1:2 molar ratio. Reaction of 1 with MOCH₃ (where M = Li, Na and K) yields bimetallic products of the type, M[(OCH₂CH₂S) )]. All these derivatives have been characterized by elemental analysis, IR, NMR (¹H and ¹³C) spectra and molar conductivity measurements. Crystals of 1 are triclinic, space group P , with a = 6.449(2), b = 10.285(2), c = 13.494(1) Å, α = 78.08(1), β = 75.99(1), γ = 71.54(2)°, V = 815.48 ų, Z = 4, D_calc = 2.239 g cm⁻³, (Mo Kα) λ = 0.7107 Å, μ = 3.55 mm₋₁, F(000) = 528, T = 295 K, final R = 0.0189 for 2344 reflections. One of the two mercaptoethanol moieties in 1 forms a five-membered chelate ring with antimony, Sb(1)---O(11) = 2.023(2) Å and Sb(1)---S(11) = 2.434(1) Å, while the other is bonded through the S atom only, Sb(1)---S(12) = 2.434(1) Å. The angles between these primary bonds with a mean value of 90.2° suggest a basically pyramidal, or pseudo tetrahedral structure if the stereochemically active lone pair is included in the coordination sphere. Two molecules are linked by intermolecular hydrogen bridges. The presence of weak intermolecular secondary bonding, Sb(1)---O(12) = 2.567(3) Å, in the complex indicates that the overall coordination polyhedron is best described in terms of a distorted trigonal bipyramidal arrangement.     

Crystallization and Preliminary X-Ray Analysis of Borrelia burgdorferi Outer Surface Protein A (OspA) Complexed with a Murine Monoclonal Antibody Fab Fragment

The Borrelia burgdorferi outer surface lipoprotein OspA is a current focus for vaccine development to prevent Lyme disease infection. A soluble, recombinant form of the protein lacking the aminoterminal lipid membrane anchor was cocrystallized with the Fab fragment of an agglutinating mouse monoclonal antibody. The crystals belong to space group P2₁2₁2₁, with a = 90.0 Å, b = 91.9 Å, and c = 102.9 Å and they were found to diffract to a maximum resolution of 2.8 Å using synchrotron radiation.     

An X-ray crystallographic study of α-d-allopyranosyl α-d-allopyranoside · CaCl2 · 5H2O (a pentadentate complex)

Three-dimensional, single-crystal, X-ray diffraction methods were used to determine the structure of the calcium chloride complex of α-d-allopyranosyl α-d-allopyranoside. The crystal is monoclinic with cell dimensions: a = 16.262(5), b = 8.345(5), c = 8.298(5)Å, β = 98.428(5)Å, and z = 2. The space group is P2₁. The structure was solved by three-dimensional Patterson and Fourier methods, and was refined by least-squares techniques to give a conventional discrepancy factor of R = 0.026; 2435 diffractometer-read reflections were used. The cation was found to be in 9-fold co-ordination to O-1, O-2, O-3, O-2′, O-3′, and four water molecules.     

Synthesis and structure of an organosamarium aryloxide complex, (C5 Me5)2 Sm(OC6HMe4-2,3,5,6)

Bis(pentamethylcyclopentadienyl)samarium bis- (tetrahydrofuranate), (C₅Me₅)₂Sm(THF)₂, reacts with 2,3,5,6-tetramethylphenol in toluene to yield (C₅Me₅)₂Sm(OC₆HMe₄-2,3,5,6). The compound crystallizes in the space group P2₁/c with a = 8.725(3) Å, b=18.821(6) Å, c=18.461(6) Å, β= 111.17(2)°, V = 2827(2) ų and D_c=1.340 g cm⁻³ for Z = 4. Molecules of the aryloxide complex are monomeric and exhibit a bent metallocene structure with a nearly linear Sm---O---C(aryloxide) linkage: Sm---O = 2.13(1) Å, O---C = 1.29(2) Å, and Sm---O---C = 172.3(13)°. Reaction of the samarium complex with phenyllithium produces the previously- characterized species (C₅Me₅)₂Sm(C₆H₅)(THF).     

trans-Bis[(thiocyanato-S)(1-methylimidazoline-2(3H)-thione)-μ2-(1-methylimidazoline-2(3H)-thione)copper(I)]: preparation, thermal analysis and crystal structure

1-Methylimidazoline-2(3H)-thione (mimtH) and copper(I) thiocyanate in refluxing ethanolacetonitrile produce a colourless, diamagnetic complex, [Cu₂(mimtH)₄(SCN)₂], which crystallises in an orthorhombic cell (a=8.0724(3), b=15.9545(6), c=21.3357(8) Å), space GROUP=Pbca, Z=4, final R=0.0319 from 2427 observed reflections F>4σ_c(F)). In the dimeric complex the copper(I) atoms are pseudo-tetrahedrally coordinated by pairs of, respectively, asymmetrically μ₂-S bridging mimtH, terminal monodentate-S mimtH, (Cu---S=2.290(1) Å), and terminal monodentate-S thiocyanate, (Cu---S=2.332(1) Å). Each pair of ligands is trans-related to its partner across crystallographic centres of symmetry, consequently, each copper(I) atom has an identical S₄ donor set with angles at the metal ranging from 95.9(1)° to 121.8(1)°. The centro-symmetric Cu₂S₂ core is rhomboid with Cu---S=2.377(1) and 2.457(1) Å, Cu---S_br---Cu=72.6(1)° and Cu---Cu, S_br---S_br separation distances of 2.861(1) and 3.897(2) Å, respectively. Thermal decomposition of the complex in flowing air, (133–1000 °C), involves de-sulfurisation of mimtH and thiocyanate with concomitant production of copper(II) sulfide followed by oxidation to copper(II) oxide.     

The crystal and molecular structure of 1,6-anhydro-β-d-mannopyranose

The crystal structure of 1,6-anhydro-β-d-mannopyranose, C₆H₁₀O₅, is orthorhombic, P2₁2₁2₁, with a = 10.971(2), b = 13.935(3), c = 9.012(1) Å, V = 1377.76 »³ (MoKα, λ = 0.7107 Å), Z = 8, D_x = 1.563 M.gm⁻³, D_m = 1.565 M.gm⁻³. the structure was solved by MULTAN and refined to R(F) = 0.043 for 2355 reflections. The two symmetry-independent molecules in the unit cell have similar conformations, except for the orientation of one of the three hydroxyl groups. The conformation of the pyranose rings is ¹C₄ distorted towards E_o, and that of the anhydro rings is E. There are significant differences between the two molecules in two of the four C---O bond-lengths. These occur where there are important differences in the hydrogen-bonding environment of the oxygen atoms. The molecules are hydrogen-bonded by three linear and three bifurcated O---H···O interactions which form four-membered loops linked into infinite chains. Empirical force-field calculations with MMI-CARB reproduced the geometry of the molecules within the variations observed experimentally between the two molecules, except for a C---O bond in one of the molecules. The effect of excluding the anomeric effect from the theoretical calculations was not significant. Calculations for an intramolecularly hydrogen-bonded molecule were also carried out as a model for the molecules in a non-polar solvent.     

Crystallization and Preliminary X-Ray Diffraction Analysis of Group 5 Mite Allergen fromDermatophagoides pteronyssinus

Crystals of the 14-kDa group 5 allergen fromDermatophagoides pteronyssinus(Der p 5) have been obtained at low pH and diffract to 3-Å resolution using a conventional x-ray source. The crystals belong to tetragonal space group P4₁2₁2 or P4₃2₁2, with unit cell parametersa=b= 114 Å andc= 234 Å. A self-rotation search revealed a 432 point symmetry and thus suggested 96 molecules in one unit cell, hence 12 monomers in each asymmetric unit.     

Type IIβ Regulatory Subunit of cAMP-Dependent Protein Kinase: Purification Strategies to Optimize Crystallization

To elucidate the structural basis for important differences between types I and II regulatory subunit isoforms (RI and RII) of adenosine 3′,5′-cyclic monophosphate (cAMP)-dependent protein kinase, the full-length RIIβ isoform and five RIIβ deletion mutants were constructed, expressed, purified, and screened for crystallization. Only one of these six proteins yielded diffraction quality crystals. Crystals were grown of the RIIβ deletion mutant (Δ1–111) monomer potentially in complex with two cAMP molecules. X-ray diffraction quality data were obtained only after significant modification to existing purification procedures. Modifications required a Sepharose, not agarose, support for cAMP affinity chromatography followed by rapid, quantitative removal of free cAMP by size-exclusion chromatography under reducing conditions. Data to 2.4 Å resolution were collected at 29°C using synchrotron radiation on a single crystal measuring 0.2 × 0.3 × 1.2 mm³. Data were 99% complete. The hexagonal crystal belonged to space group P6₍₁₎ or P6₍₅₎ with unit cell dimensions a = b = 161.62 Å and c = 39.66 Å.     

Purification, Characterization, and Crystallization of anN-HydroxyarylamineO-Acetyltransferase fromSalmonella typhimurium

TheN-hydroxyarylamineO-acetyltransferase fromSalmonella typhimuriumhas been expressed as a histidine-tagged fusion protein inEscherichia coliand purified to apparent homogeneity using single-step immobilized metal ion chromatography. Sufficient quantities of the purified protein have been obtained to allow its characterization by physical methods including dynamic light scattering and electrospray mass spectrometry. The substrate specificity and temperature sensitivity of the enzymatic activity have also been assessed. The enzyme has been crystallized from sodium, potassium tartrate and X-ray diffraction data have been obtained to allow the identification of an orthorhombic unit cell, point group P2₁2₁2, with dimensionsa= 137 Å,b= 223 Å, andc= 105 Å. These crystals will provide a route to a crystallographic determination of the structure of the protein.     

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol have been determined by single-crystal X-ray diffraction studies. The space group of the α-cyclodextrin–p-chlorophenol complex is P2₁2₁2₁ with unit cell dimensions of a=15.299(3), b=24.795(5), c=13.447(5) Å, and that of the α-cyclodextrin–p-cresol complex is P2₁ with unit cell dimensions of a=7.927(7), b=13.568(7), c=24.54(1) Å, β=90.41(8)°. In spite of the similar structures of guest molecules, both complexes have different inclusion modes and packing structures.     

Purification, crystallization and preliminary X-ray diffraction studies of the bacteriophage φ29 connector particle

The connector or portal particle from double-stranded DNA bacteriophage φ29 has been crystallized. This structure, which connects the head of the virus with the tail and plays a central role in prohead assembly and DNA packaging and translocation, is formed by 12 subunits of the p10 protein and has a molecular weight of 430 kDa. The connector structure was proteolysed with endoproteinase Glu-C from Staphylococcus aureus V8, which removes 13 and 18 amino acids from the amino- and carboxy-terminal regions of the p10 protein, respectively. Two crystal forms were grown from drops containing an alcohol solution and paraffin oil. Crystals of form I are monoclinic, space group C2 with cell dimensions a=416.86 Å, b=227.62 Å, c=236.68 Å and β=96.3° and contain four connector particles per asymmetric unit. Crystals of form II are tetragonal, space group P4₂2₁2 with cell dimensions a=b=170.2 Å, c=156.9 Å and contain half a particle per asymmetric unit. X-ray diffraction data from both native crystal forms have been collected to 6.0 and 3.2 Å respectively, using synchrotron radiation. Crystals of form II are likely to have the same packing arrangement as the two-dimensional crystals analyzed previously by electron microscopy.     

Molecular conformation of prostaglandin A1 monoclinic cyrstalline polymorph

The molecular conformation of the monoclinic crystalline polymorph of prostaglandin A₁ has been determined by X-ray diffraction techniques. The space group is P2₁ with a = 13.637 (2), b = 7.567 (1), I c = 10.576 (2) Å, β = 107.37 (3)°; D_c = 1.073 g·cm⁻³ for Z = 2. The molecular conformation is characterized by the nearly parallel arrangement of the C₁–C₇ and C₁₃–C₂₀ side chains, with a general flattening of the overall structure when compared with the orthorhombic polymorph. The cyclopentenone moiety assumes a C₈ envelope conformation with C₈ and O₉ displaced +0.29 Å and −0.18 Å from the C₉–C₁₀=C₁₁–C₁₂ plane respectively. Concerted, small variations of the torsion angles, primarily about the C₈–C₁₂, C₁₄–C₁₅ and C₁₆–C₁₇ bonds, bring the monoclinic and orthorhombic conformations into coincidence.     

Synthesis, crystal structure, antitumor activity and DNA-binding study on the Mn(II) complex of 2H-5-hydroxy-1,2,5-oxadiazo[3,4-f]1,10-phenanthroline

The complex [Mn(L)(NO₃)₂(H₂O)₂] (1) (L=2H-5-hydroxy-1,2,5-oxadiazo[3,4-f]1,10-phenanthroline) was synthesized and characterized by elemental analysis, IR and UV. The crystal and molecular structure of 1 was determined by single-crystal X-ray diffraction; crystal data: light yellow, monoclinic, space group P2₁/n, Z=4, a=7.432(2) Å, b=9.582(3) Å, c=23.445(7) Å, β=90.519(5)°. The Mn atom in 1 is hexa-coordinated in a distorted octahedral arrangement by two N atoms of the ligand L and four O atoms of two water molecules and two nitrate anions. Biological tests in vitro showed that 1 has significant antitumor activity against HL-60, KB, Hela and BGC-823 cells. The interaction of 1 with calf thymus DNA was investigated by absorption titration, thermal denaturation and viscosity measurements. The results suggest that 1 binds with DNA by intercalating via the ligand L.     

Metal dependent coordination of biomolecular ligand: X-ray crystal structures of copper, cobalt and calcium complexes of (3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinic acid) 5-phosphate, an oxidized pyridoxal 5-phosphate

X-ray crystal analyses of divalent copper, cobalt and calcium complexes of monoanionic (3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinic acid) 5-phosphate (L₁C₈H₉NO₇P⁻) revealed the chemical compositions of Cu ---L·3H₂O(1), Co ---L·5H₂O(2) and Ca·L₂·7H₂O (3) and the coordination structures which depend on the coordination abilities and chemical properties of the respective metal ions. Although 1 and 2 crystals showed similar features, i.e., presence of the metal ion at the crystallographic center of symmetry and octahedral six-coordination, the patterns of coordination with the ligand molecules differed. While direct coordination to the L carboxyl oxygen was observed in 1 crystals, all ligation positions in 2 crystals were occupied by water molecules. On the other hand, 3 crystals formed a pentagonal bipyramidal structure (seven-coordination), where oxygens of L phosphates and water molecules coordinated to the calcium ion. Each of the complex structures showed characteristic molecular packing depending on the pattern of coordination to the respective metal ion. L is monoanionic in all complex crystals, where the phosphate and carboxyl groups are deprotonated and pyridine nitrogen is protonated, and is neutralized by each metal ion. Crystal data: 1, monoclinic, space group P2₁/c, A = 5.4129(6), B = 10.515(2), C = 22.770(2) Å, β = 91.853(9)°, Z = 4, R = 0.0404 for 1834 observed reflections; 2, triclinic, space group

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, c = 6.789(3) Å, α = 96.84(3), β = 109.10(3), γ = 100.50(2)°, Z = 2, R = 0.0684 for 1605 observed reflections; 3, triclinic, , a = 10.069(2), B = 14.501(3), c = 10.051(1) Å, α = 100.75(1), β = 97.28(2), γ = 76.18(2)°, Z = 2, R = 0.0540 for 3637 observed reflections.     

Synthesis and crystal structure of the MgCl2(CH3COOC2H5)2· (CH3COOC2H5) adduct

The reaction of α-MgCl₂ with boiling ethyl acetate affords MgCI₂(CH₃COOC₂H₅)₂· (CH₃COOC₂H₅), which is obtained as crystals suitable for X-ray analysis only from the mother liquor. M=315.5, orthorhombic, space group P2₁22₁ (No. 18), a=25.077(3), b=8.616(1), c=7.345(1) Å, V=1587.0(3) ų, Z=4, D_x=1.32 g cm⁻³,λ A(Mo Kα)=0.71069 Å, μ=4.17 cm⁻¹, F(000)=664, T=298 K, observed reflections: 1667, R=0.059 and R_w=0.069. The structure is composed of polymeric chains of MgCl₂(CH₃COOC₂H₅₎₂ and the ethyl acetate molecules occupy a mutually trans position.     

Structural analysis of 6-S-(benzoxazol-2-yl)-6-deoxy

The reactive palladium dimer, [Pd(dppm)(O₂CCF₃)]₂, is carbonylated to [Pd(dppm)(O₂CCF₃)]₂(μ-CO) in a reversible reaction with K = c. 7.2(2)x10⁴ atm⁻¹ (P_1/2 = c. 2.4 Torr). This is significantly larger than is expected based on the λ_max = 280 nm in the electronic spectrum. The product can be isolated in analytically pure form by crystallization under a CO atmosphere. It forms crystals in the monoclinic space group Cc with a = 18.584(5), b = 28.65(1), c = 11.164(3) Å and β = 95.16(2)°. The structure is significantly distorted. The bonding about the two palladium atoms is quite asymmetric. While one is close to a square planar geometry with a Pd---C(O) distance of 1.90(2) Å, the other is significantly pyramidalized and has a longer (2.00(2) Å) bond to the bridging CO. The Pd---Pd distance is only 2.896(2) Å, much shorter than that usually observed for formally non-bonded Pd atoms.     

Anomalous carbonylation of [Pd(dppm)(O2CCF3)]2 to give an asymmetric μ-CO complex

The reactive palladium dimer, [Pd(dppm)(O₂CCF₃)]₂, is carbonylated to [Pd(dppm)(O₂CCF₃)]₂(μ-CO) in a reversible reaction with K = c. 7.2(2)x10⁴ atm⁻¹ (P_1/2 = c. 2.4 Torr). This is significantly larger than is expected based on the λ_max = 280 nm in the electronic spectrum. The product can be isolated in analytically pure form by crystallization under a CO atmosphere. It forms crystals in the monoclinic space group Cc with a = 18.584(5), b = 28.65(1), c = 11.164(3) Å and β = 95.16(2)°. The structure is significantly distorted. The bonding about the two palladium atoms is quite asymmetric. While one is close to a square planar geometry with a Pd---C(O) distance of 1.90(2) Å, the other is significantly pyramidalized and has a longer (2.00(2) Å) bond to the bridging CO. The Pd---Pd distance is only 2.896(2) Å, much shorter than that usually observed for formally non-bonded Pd atoms.