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PubMed2005

Structure of d(TGCGCG).d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA.

The sequence d(TGCGCG).d(CGCGCA) crystallized in two crystal forms, orthorhombic and hexagonal, in the presence of cobalt hexammine chloride, a known inducer of the left-handed Z-form of DNA. The crystal structures have been solved and refined at 1.71 A resolution in space group P2(1)2(1)2(1) and 2.0 A resolution in space group P6(5). The orthorhombic structure contains one Z-DNA hexamer duplex, while the hexagonal structure contains two hexamer duplexes in the structure. Of the latter, one is situated on a crystallographic sixfold screw axis, leading to disorder. This paper reports the effects of sequence and crystal packing on the structure of Z-type DNA. The structures lend additional support to the authors' earlier conclusion that a stretch of four C.G base pairs is sufficient to nucleate and define the regular model of the left-handed helix based on the structure of d(CGCGCG)2.

Base Pairing↗
PubMed1994

Crystallization experiments with 2-enoyl-CoA hydratase, using an automated 'fast-screening' crystallization protocol.

A convenient method for screening crystallization conditions using an automated fast-screen protocol has been implemented and tested on an enoyl-CoA hydratase. The crystallization solutions for the initial screening and subsequent optimizations are prepared using a crystallization robot. Enoyl-CoA hydratase (E.C. 4.2.1.17), purified from rat-liver mitochondria, is one of the enzymes from the beta-oxidation pathway of fatty-acid metabolism; it catalyzes the reversible hydration of 2-trans-enoyl-CoA's to L-3-hydroxy-acyl-CoA's. Different crystal forms, diffracting to 3.0 A, were obtained.

Journal Article↗
PubMed1994

Crystallization and X-ray structure determination of cytochrome c2 from Rhodobacter sphaeroides in three crystal forms.

Cytochrome c(2) serves as the secondary electron donor that reduces the photo-oxidized bacteriochlorophyll dimer in photosynthetic bacteria. Cytochrome c(2) from Rhodobacter sphaeroides has been crystallized in three different forms. At high ionic strength, crystals of a hexagonal space group (P6(1)22) were obtained, while at low ionic strength, triclinic (P1) and tetragonal (P4(1)2(1)2) crystals were formed. The three-dimensional structures of the cytochrome in all three crystal forms have been determined by X-ray diffraction at resolutions of 2.20 A (hexagonal), 1.95 A, (triclinic) and 1.53 A (tetragonal). The most significant difference observed was the binding of an imidazole molecule to the iron atom of the heme group in the hexagonal structure. This binding displaces the sulfur atom of Met l00, which forms the axial ligand in the triclinic and tetragonal structures.

Journal Article↗
PubMed1996

Crystallization and preliminary X-ray analysis of twinned crystals of a chimeric FK506 binding protein 12 and 13 complexed with FK506.

An FKBPI2/13 chimera with the 80s loop of FKBPI3 replacing the corresponding loop in FKBPI2 tightly binds the immunosuppressive agents FK506 and rapamycin and efficiently catalyzes peptidyl-prolyl cis-trans isomerization. However, the chimera's complex with FK506 does not inhibit calcineurin's phosphatase activity [Yang, Rosen & Schreiber (1993). J. Am. Chem. Soc. 115(2), 819-820]. The chimeric protein crystallizes in space group P1 and the crystals are always twinned. The twin composites are related by a twofold twinning axis parallel to the a axis. A resolution data set (1.5 A resolution) for a twinned crystal was collected at CHESS using 0.91 A X-rays and image plates. Preliminary molecular replacement using data between 15 and 3 A and the FKBPI2-FK506 crystal structure as the search model led to a clear solution with a residual of 34.2%. This 3 A resolution structure provides insight into the structural basis of twinning.

Journal Article↗
PubMed1996

Crystallization and preliminary X-ray study of a new crystal form of cytochrome c' from Rhodobacter capsulatus.

A new crystal form of diheme cytochrome c' from Rhodobacter capsulatus has been obtained and preliminary crystallographic experiments have been performed. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions of a = 47.82, b = 72.59, c = 34.32 A. The assumption that an asymmetric unit of the crystal contains one half of the homodimer molecule indicates that the monomers in the dimeric molecule may be related by a crystallographic twofold axis. Crystals diffract up to 1.7 A resolution using the X-ray beam from synchrotron radiation, and 11 127 unique structure factors were obtained with an R(merge) of 7.1% from 52 922 indexed reflections. Structure analysis by means of molecular-replacement methods is now underway.

Journal Article↗
PubMed1996

Crystallization and preliminary X-ray analysis of two new crystal forms of calmodulin.

Two new crystal forms of calmodulin from Gallus gallus are reported. Crystals in space group P1 (cell dimensions a = 59.7, b = 53.1, c = 24.6 A, alpha = 93.2, beta = 96.7, gamma = 89.2 and Z = 2), grow as long thin needles. Water content on density considerations is approximately 50%. They diffract to approximately 2.0 A but give wide multiply peaked spot profiles. Crystals in space group P2(1)2(1)2(1) (cell dimensions a = 32.2, b = 56.0, c = 67.3 A and Z = 4), grow as clusters of thin tablets and contain approximately 30% water by volume. These small crystals ( approximately 0.4 x 0.15 x 0.1 mm) diffracted well to approximately 1.4 A and some appreciable intensities were observed at resolutions better than 1.2 A.

Journal Article↗
PubMed1996

Crystallization and crystal packing of recombinant 3 (or 17) beta-hydroxysteroid dehydrogenase from Comamonas testosteroni ATTC 11996.

The enzyme 3 (or 17) beta-hydroxysteroid dehydrogenase from Comamonas testosteroni was crystallized. Crystals, of up to 0.6 mm in their longest dimension and suitable for a crystallographic analysis have been obtained by the vapour diffusion method. They belong to the orthorhombic lattice type and diffract to a maximum resolution of 0.23 nm. A final data set obtained by merging data from three crystals resulted in a completeness of 90% with an Rmerge of 6%. A molecular replacement search carried out by using 3 alpha (or 20 beta)-hydroxysteroid dehydrogenase from Streptomyces hydrogenans as a search model allowed us to assign I222 as the correct space group and to propose a model for the crystal packing, with one monomer per asymmetric unit. Thus, the whole unit cell contains two tetramers. The R-factor after rigid body refinement is 48.1%.

17-Hydroxysteroid Dehydrogenases↗
PubMed2002

Branched crystal morphology of linear polyethylene crystallized in a two-dimensional diffusion-controlled growth field.

The branched crystal morphology of linear polyethylene formed at various temperatures from thin films has been studied by atomic-force microscopy (AFM), transmission electron microscopy (TEM), electron diffraction (ED) pattern and polymer decoration technique. Two types of branched patterns, i.e. dendrite and seaweed patterns, have been visualized. The fractal dimension d(f) = 1.65 of both dendrite and some of seaweed patterns was obtained by using the box-counting method, although most of the seaweed patterns are compact. Selected-area ED patterns indicate that the fold stems tilt about 34.5( degrees ) around the b-axis and polymer decoration patterns show that the chain folding direction and regularity in two (200) regions are quite different from each other. Because of chain tilting, branched crystals show three striking features: 1) the lamella-like branches show two (200) regions with different thickness; 2) the crystals usually bend towards the thin region; 3) the thick region grows faster by developing branches, thus branches usually occur outside the thick region. The branched patterns show a characteristic width w, which gives a linear relationship with the crystallization temperature on a semilogarithmic plot.

Journal Article↗
PubMed2003

Crystallization kinetics and crystal morphology in thin poly(ethylene oxide) films.

We present a detailed study of the kinetics of crystallization for thin films of poly(ethylene oxide) (PEO). Measurements of the growth rate have been carried out using optical-microscopy techniques on films of monodisperse PEO. Films with thicknesses from 13 nm to approximately 2 microm were crystallized isothermally at temperatures approximately 20 degrees C below the melting point. A remarkable non-monotonic slowing-down of the crystal growth is observed for films with thickness less than approximately 400 nm. The changes in the growth rate from bulk-like values is significant and corresponds to a factor of 40 decrease for the thinnest films studied. The morphologies of isothermally crystallized samples are studied using atomic-force microscopy. We find that a morphology, similar to diffusion-controlled growth (dendritic growth and densely branched growth), is observed for films with h<150 nm. In addition, changes in the morphology occur for thicknesses consistent with changes in the growth rate as a function of film thickness.

Journal Article↗
PubMed1996

The crystallization and Preliminary Crystallographic Analysis of the Monoclinic Crystal Form of Basic Phospholipase A(2) from the Venom of Agkistrodon halys Pallas.

The basic phospholipase A(2) from the venom of Agkistrodon halys Pallas exhibits strong hemolytic activity. The enzyme has been crystallized by vapour diffusion techniques. Diffraction data of the crystal have been collected up to 2.5 Aring; resolution using the synchrotron radiation-imaging plate-Weissenberg camera system. The crystal parameters were calculated with an auto-indexing program. The crystal belongs to C2 space group with unit cell dimensions of alpha=100.38 Aring;, b=54.37 Aring;, c=117.38 Aring; and beta=120.71 deg;. Each asymmetric unit probably contains four or five molecules.

Journal Article↗
PubMed1977

[Protein crystals and tubuli bundles in yeast cells. VI. Light-and electron microscopy studies as well as biochemical studies on alcohol dehydrogenase activity of isolated crystals].

Isolated crystals from Saccharomyces carlsbergensis, stabilized by Cd2+ or Zn2+, retain their enzymatic activity as shown by topochemical reactions. During these reactions the crystals disintegrate characteristically. Stages of this disintegration and deposition of reaction products have been demonstrated by light and electron microscopy. Ground plasmatic and mitochondrial alcoholdhydrogenase has been solubilized by means of 0.01 M EDTA from Zn2+ stabilized crystals separated by gel electrophoresis and proved to be active.

Alcohol Oxidoreductases↗
PubMed1991

Characterization of polymorphs of tranilast anhydrate and tranilast monohydrate when crystallized by two solvent change spherical crystallization techniques.

Spherically agglomerated crystals of tranilast (oral antiallergic agent) with improved availability in vitro, as well as improved micromeritic properties such as flowability and packability, were prepared by a novel spherical crystallization technique. The agglomerates of tranilast were found to be composed of new monohydrate I, II, or III, depending on the crystallization solvent and the procedure employed. With dehydration by heating, monohydrate I transformed to the stable alpha form directly. On the other hand, monohydrates II and III converted to the amorphous and beta forms, respectively, followed by further transformation to the alpha form at 110 and 150 degrees C, respectively. The amorphous and beta forms of agglomerates were easily prepared by storing the monohydrates under 0% RH at 30-40 degrees C. Monohydrate II and the amorphous form of the agglomerate with high surface energy could enhance the solubility and the dissolution rate of tranilast. A phase diagram of polymorphs of agglomerated tranilast was constructed to exhibit their interconversions under various humidities and temperatures.

Chemical Phenomena↗
PubMed1988

Crystallization and preliminary investigation of single crystals of deoxyuridine triphosphate nucleotidohydrolase from Escherichia coli.

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase), an enzyme in the nucleotide metabolism that is a pyrophosphatase hydrolyzing dUTP, has been crystallized. The crystals belong to the trigonal space group R3 and diffract beyond 2 A. The native dUTPase crystals and a mercury derivative are stable in the X-ray beam and are suitable for a high resolution X-ray structure analysis.

Amino Acid Sequence↗
PubMed1993

Crystallization and preliminary X-ray diffraction analysis of crystals of Thermoascus aurantiacus xylanase.

Crystals suitable for high resolution X-ray diffraction analysis have been grown of the 29,774-Da protein, xylanase (1,-4-beta-xylan xylanohydrolase EC 3.2.1.8) from the thermophilic fungus Thermoascus aurantiacus. This protein, an endoxylanase demonstrates the hydrolysis of beta-(1-4)-D-xylose linkage in xylans and crystallizes as monoclinic pinacoids in the presence of ammonium sulphate buffered at pH 6.5, and also with neutral polyethylene glycol 6000. The crystals belong to space group P2(1) and have cell dimensions, a = 41.2 A, b = 67.76 A, c = 51.8 A; beta = 113.2 degrees.

Ascomycota↗
PubMed1994

Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes.

Fab fragments from Jel 103, an antibody which specifically binds to single-stranded poly(rl), were prepared by papain digestion, separated into eight isoforms and characterized by mass spectrometry. One of the purified isoforms yielded crystals suitable for structural studies by X-ray diffraction and its crystal structure was determined to 2.4 A resolution. Soaking the crystals in solutions containing either of the mononucleotides inosine-5'-diphosphate, guanosine-5'-diphosphate or deoxyinosine-5'-monophosphate resulted in binding of the nucleotide in a single binding site. However, adenosine-5'-diphosphate does not bind to this antibody. The recognition of the base is achieved through hydrogen bonds to the C6 carbonyl oxygen and the imino NH group of the purine in a pattern similar to that of the base-base interactions in a double-stranded nucleic acid. Additional binding energy is provided by stacking of the base and the Tyr32L side-chain and by interaction of the alpha-phosphate with the antibody in an anionic binding site. Most of the side-chains interacting with the nucleotide come from the light chain. Surprisingly, this antibody shares the VL sequence with another nucleic acid-binding antibody, BV04-1. The latter binds to a single stranded DNA with a high preference for thymine bases. The structures of the unliganded and complexed Jel 103 Fab are compared to those of BV-04-1 Fab and while they show similarity in recognition of the base of the immunodominant nucleotide, their 5' phosphates occupy different positions, suggesting different orientation of the nucleic acid bound to these two antibodies. Differences in the conformations of the L1 loops between the two Fabs have been noted.

Amino Acid Sequence↗
PubMed1994

Crystallization and preliminary X-ray analysis of a new crystal form of nitrite reductase from Pseudomonas aeruginosa.

Nitrite reductase from Pseudomonas aeruginosa (EC 1.9.3.2), a redox enzyme synthesized by the bacterium grown in the presence of nitrate, is a soluble dimer of two identical subunits of 60 kDa, each containing one c and one d1 haem as prosthetic groups. A new crystal from of the Ps. aeruginosa nitrite reductase in the oxidized state, suitable for X-ray structure determination, has been obtained by vapour diffusion at 20 degrees C, in the presence of 10% polyethylene glycol 4000, 50 mM Tris-HCl (pH 8.7), 400 mM NaCl and at a protein concentration of 14 mg/ml. The crystals are dark green elongated tetragonal prisms of dimensions 1.5 mm x 0.2 mm x 0.2 mm for the largest ones. These crystals are tetragonal with space group P4(1(3))2(1)2 and cell dimensions a = b = 128.2 A, c = 172.6 A. They diffract at least up to 2.8 A. Assuming a dimer in the asymmetric unit, the VM value is 2.95 A3/Da (58% of solvent).

Crystallization↗
PubMed1994

Crystallization and preliminary X-ray diffraction studies of the lepidopteran-specific insecticidal crystal protein CrylA(a).

A trypsin-activated CrylA(a) protein from Bacillus thuringiensis has been purified and crystallized. Crystals belong to orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 53.3, b = 111.3 and c = 154.7 A. The crystals diffract to at least 2.2 angstrum resolution and are suitable for X-ray structural analysis. They contain a single molecule in the asymmetric unit.

Animals↗
PubMedDate not supplied

A novel method for transfer of two-dimensional crystals from the air/water interface to specimen grids. EM sample preparation/lipid-layer crystallization.

Transfer of two-dimensional (2-D) crystals formed on lipid layers by suspension from a wire loop is described. This method gives better recovery and better preservation of 2-D crystals than attained in the past. The method has been applied to crystals of yeast RNA polymerase II to enable their analysis in the frozen hydrated state.

Air↗