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Complete Diffraction Data Set (complete + diffraction_data_set)
Selected AbstractsCrystals of ternary protein,DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBP, or C/EBP, and tom-1A promoter fragmentACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001Tahir H. Tahirov c-Myb and the C/EBP family are transcriptional regulatory factors that act in concert to regulate the expression of myeloid-specific genes. v-Myb encoded by avian myeloblastosis virus (AMV) is a mutated form of c-Myb that contains point mutations which disrupt the cooperation with C/EBPs. To understand the mechanism of the transcriptional synergy between c-Myb and C/EBPs and the effect of the v-Myb mutations on that synergy, knowledge based on their three-dimensional structures is essential. Crystals of ternary complexes, in which various combinations of the DNA-binding domains of c-Myb or v-Myb and C/EBP, or C/EBP, are bound to a DNA fragment from tom-1A promoter, were obtained by the vapour-diffusion method. Complete diffraction data sets were obtained from each native crystal and two types of iodine-derivative crystals. A three-wavelength MAD data set was also obtained from a bromine-derivative crystal. [source] Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNAACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2006Marina N. Vassylyeva The bacterial transcriptional factor and virulence regulator RfaH binds to rapidly moving transcription elongation complexes through specific interactions with the exposed segment of the non-template DNA strand. To elucidate this unusual mechanism of recruitment, determination of the three-dimensional structure of RfaH and its complex with DNA was initiated. To this end, the Escherichia coli rfaH gene was cloned and expressed. The purified protein was crystallized by the sitting-drop vapor-diffusion technique. The space group was P6122 or P6522, with unit-cell parameters a = b = 45.46, c = 599.93,Å. A complex of RfaH and a nine-nucleotide oligodeoxyribonucleotide was crystallized by the same technique, but under different crystallization conditions, yielding crystals that belonged to space group P1 (unit-cell parameters a = 36.79, b = 44.01, c = 62.37,Å, , = 80.62, , = 75.37, , = 75.41°). Complete diffraction data sets were collected for RfaH and its complex with DNA at 2.4 and 1.6,Å resolution, respectively. Crystals of selenomethionine-labeled proteins in both crystal forms were obtained by cross-microseeding using the native microcrystals. The structure determination of RfaH and its complex with DNA is in progress. [source] Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2006Anna A. Perederina The Escherichia coli gene encoding the transcription cleavage factor GreB and the Thermus thermophilus gene encoding the anti-GreA transcription factor Gfh1 were cloned and expressed and the purified proteins were crystallized by the sitting-drop vapor-diffusion technique. The GreB and Gfh1 crystals, which were improved by macroseeding, belong to space group P41212 (or P43212), with unit-cell parameters a = b = 148, c = 115.2,Å and a = b = 59.3, c = 218.9,Å, respectively. Complete diffraction data sets were collected for the GreB and Gfh1 crystals to 2.6 and 2.8,Å resolution, respectively. Crystals of the selenomethionine proteins were obtained by microseeding using the native protein crystals and diffract as well as the native ones. The structure determination of these proteins is now in progress. [source] The minimum crystal size needed for a complete diffraction data setACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010James M. Holton In this work, classic intensity formulae were united with an empirical spot-fading model in order to calculate the diameter of a spherical crystal that will scatter the required number of photons per spot at a desired resolution over the radiation-damage-limited lifetime. The influences of molecular weight, solvent content, Wilson B factor, X-ray wavelength and attenuation on scattering power and dose were all included. Taking the net photon count in a spot as the only source of noise, a complete data set with a signal-to-noise ratio of 2 at 2,Å resolution was predicted to be attainable from a perfect lysozyme crystal sphere 1.2,µm in diameter and two different models of photoelectron escape reduced this to 0.5 or 0.34,µm. These represent 15-fold to 700-fold less scattering power than the smallest experimentally determined crystal size to date, but the gap was shown to be consistent with the background scattering level of the relevant experiment. These results suggest that reduction of background photons and diffraction spot size on the detector are the principal paths to improving crystallographic data quality beyond current limits. [source] Purification, crystallization and preliminary X-ray analysis of Triatoma virus (TrV) from Triatoma infestansACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Gabriela S. Rozas-Dennis Triatoma virus (TrV) is a viral pathogen of the blood-sucking reduviid bug Triatoma infestans, the most important vector of American human trypanosomiasis (Chagas' disease). TrV has been putatively classified as a member of the Cripavirus genus (type cricket paralysis virus) in the Dicistroviridae family. This work describes the purification of TrV particles from infected T. infestans and their crystallization and preliminary crystallographic analyses. Two different crystal forms, rhombohedral and orthorhombic, were obtained at room temperature by the hanging-drop vapour-diffusion technique using polyethylene glycol and polyethylene glycol monomethylether as precipitants. The rhombohedral crystals have unit-cell parameters a = b = 306.6, c = 788.4,Å (hexagonal setting), diffract to 3.2,Å resolution and contain one-third of the viral particle per asymmetric unit. The orthorhombic crystals have cell parameters a = 336, b = 351, c = 332,Å, diffract to about 2.5,Å resolution, and contain one-half of a virus particle in the asymmetric unit. A complete diffraction data set has been collected to 3.2,Å resolution, using synchrotron radiation, from a single rhombohedral crystal under cryogenic conditions. [source] Expression, purification, crystallization and preliminary X-ray crystallographic studies of a psychrophilic cellulase from Pseudoalteromonas haloplanktisACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Sébastien Violot The Antarctic psychrophile Pseudoalteromonas haloplanktis produces a cold-active cellulase. To date, a three-dimensional structure of a psychrophilic cellulase has been lacking. Crystallographic studies of this cold-adapted enzyme have therefore been initiated in order to contribute to the understanding of the molecular basis of the cold adaptation and the high catalytic efficiency of the enzyme at low and moderate temperatures. The catalytic core domain of the psychrophilic cellulase CelG from P. haloplanktis has been expressed, purified and crystallized and a complete diffraction data set to 1.8,Å has been collected. The space group was found to be P212121, with unit-cell parameters a = 135.1, b = 78.4, c = 44.1,Å. A molecular-replacement solution, using the structure of the mesophilic counterpart Cel5A from Erwinia chrysanthemi as a search model, has been found. [source] Purification, crystallization and preliminary crystallographic analysis of very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Zhijie Li Acyl-CoA dehydrogenase [acyl-CoA:(acceptor) 2,3-oxidoreductase; EC 1.3.99.3] catalyzes the first reaction step in mitochondrial fatty-acid ,-oxidation. Here, the very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans (cVLCAD) has been cloned and overexpressed in Escherichia coli strain BL21 (DE3). Interestingly, unlike other very-long-chain acyl-CoA dehydrogenases, cVLCAD was found to form a tetramer by size-exclusion chromatography coupled with in-line static light-scattering, refractive-index and ultraviolet measurements. Purified cVLCAD (12,mg,ml,1) was successfully crystallized by the hanging-drop vapour-diffusion method under conditions containing 100,mM Tris,HCl pH 8.0, 150,mM sodium chloride, 200,mM magnesium formate and 13% PEG 3350. The crystal has a tetragonal form and a complete diffraction data set was collected and processed to 1.8,Å resolution. The crystal belonged to space group C2, with unit-cell parameters a = 138.6, b = 116.7, c = 115.3,Å, , = , = 90.0, , = 124.0°. A self-rotation function indicated the existence of one noncrystallographic twofold axis. A preliminary molecular-replacement solution further confirmed the presence of two molecules in one asymmetric unit, which yields a Matthews coefficient VM of 2.76,Å3,Da,1 and a solvent content of 55%. [source] Crystallization and preliminary X-ray crystallographic analysis of ,-galactosidase from Kluyveromyces lactisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Ángel Pereira-Rodríguez ,-Galactosidase from Kluyveromyces lactis catalyses the hydrolysis of the ,-galactosidic linkage in lactose. Owing to its many industrial applications, the biotechnological potential of this enzyme is substantial. This protein has been expressed in yeast and purified for crystallization trials. However, optimization of the best crystallization conditions yielded crystals with poor diffraction quality that precluded further structural studies. Finally, the crystal quality was improved using the streak-seeding technique and a complete diffraction data set was collected at 2.8,Å resolution. [source] Purification and crystallization of the entire recombinant subunit E of the energy producer A1Ao ATP synthaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Asha Manikkoth Balakrishna A1Ao ATP synthases are the major energy producers in archaea. Subunit E of the stator domain of the ATP synthase from Pyrococcus horikoshii OT3 was cloned, expressed and purified to homogeneity. The monodispersed protein was crystallized by vapour diffusion. A complete diffraction data set was collected to 3.3,Å resolution with 99.4% completeness using a synchrotron-radiation source. The crystals belonged to space group I4, with unit-cell parameters a = 112.51, b = 112.51, c = 96.25,Å, and contained three molecules in the asymmetric unit. [source] Crystallization and preliminary X-ray diffraction data of ,-galactosidase from Saccharomyces cerevisiaeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Rafael Fernández-Leiro Saccharomyces cerevisiae,-galactosidase is a highly glycosylated extracellular protein that catalyzes the hydrolysis of ,-galactosidic linkages in various glucids. Its enzymatic activity is of interest in many food-related industries and has biotechnological applications. Glycosylated and in vitro deglycosylated protein samples were both assayed for crystallization, but only the latter gave good-quality crystals that were suitable for X-ray crystallography. The crystals belonged to space group P4212, with unit-cell parameters a = b = 101.24, c = 111.52,Å. A complete diffraction data set was collected to 1.95,Å resolution using a synchrotron source. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from Staphylococcus aureus NCTC 8325ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Sudipta Bhattacharyya An atypical two-cysteine peroxidase, SAOUHSC_01822, from the virulent Staphylococcus aureus strain NCTC 8325 plays a major role in the reponse of the bacterium to oxidative stress. The protein was cloned, expressed, purified to homogeneity and crystallized. The protein was crystallized from 2,M ammonium sulfate, 0.1,M Na HEPES pH 7, 2%(v/v) PEG 400. A complete diffraction data set was collected to 2.3,Å resolution using a Rigaku MicroMax HF007 Cu,K, X-ray generator and a Rigaku R-AXIS IV++ detector. The crystals belonged to space group P21, with unit-cell parameters a = 43.50, b = 149.35, c = 73.73,Å, , = 104.4°, and contained four molecules in the asymmetric unit. [source] | ||||||||||