Home About us Contact
|
Home About us Contact | ||
|
|
||
Solvent Content (solvent + content)
Kinds of Solvent Content Selected AbstractsMethacrylate-based monolithic column with mixed-mode hydrophilic interaction/strong cation-exchange stationary phase for capillary liquid chromatography and pressure-assisted CECELECTROPHORESIS, Issue 19 2008Jian Lin Abstract A novel porous polymethacrylate-based monolithic column by in situ copolymerization of 3-sulfopropyl methacrylate (SPMA) and pentaerythritol triacrylate in a binary porogenic solvent consisting of cyclohexanol/ethylene glycol was prepared. The monolith possessed in their structures bonded sulfonate groups and hydroxyl groups and was evaluated as a hydrophilic interaction and strong cation-exchange stationary phases in capillary liquid chromatography (cLC) and pressure-assisted CEC using small polar neutral and charged solutes. While the SPMA was introduced as multifunctional monomer, the pentaerythritol triacrylate was used to replace ethylene glycol dimethacrylate as cross-linker with much more hydrophilicity due to a hydroxyl sub-layer. The different characterization of monolithic stationary phases were specially designed and easily prepared by altering the amount of SPMA in the polymerization solution as well as the composition of the porogenic solvent for cLC and pressure-assisted CEC. The resulting monolith showed the different trends about the effect of the permeabilities on efficiency in the pressure-assisted CEC and cLC modes. A typical hydrophilic interaction chromatography mechanism was observed at higher organic solvent content (ACN%>70%) for polar neutral analytes. For polar charged analytes, both hydrophilic interaction and electrostatic interaction contributed to their retention. Therefore, for charged analytes, selectivity can be readily manipulated by changing the composition of the mobile phase (e.g., pH, ionic strength and organic modifier). With the optimized monolithic column, high plate counts reaching greater than 170,000,plates/m for pressure-assisted CEC and 105,000 plates/m for cLC were easily obtained, respectively. [source] Structure of d -tyrosyl-tRNATyr deacylase using home-source Cu,K, and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme statesACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Manickam Yogavel d -Tyrosyl-tRNATyr deacylase (DTD) is an editing enzyme that removes d -amino acids from mischarged tRNAs. The crystal structure of Plasmodium falciparum DTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10,30,s in cryoprotectant solution containing 0.2,1,M NaI. Iodide-SAD data sets were collected to 3.3 and 2.74,Å resolution from PfDTD crystals that belonged to two different space groups, P43 and P1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinic P1 and tetragonal P43 space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps using PHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83,Å resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity. [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] Structure of the X (ADRP) domain of nsp3 from feline coronavirusACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Justyna A. Wojdyla The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2,Å resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9,Å resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a. [source] Prospects for de novo phasing with de novo protein modelsACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Rhiju Das The prospect of phasing diffraction data sets `de novo' for proteins with previously unseen folds is appealing but largely untested. In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance in molecular replacement with the Phaser software. 15 new cases of diffraction data sets that are unambiguously phased with de novo models are presented. These diffraction data sets represent nine space groups and span a large range of solvent contents (33,79%) and asymmetric unit copy numbers (1,4). No correlation is observed between the ease of phasing and the solvent content or asymmetric unit copy number. Instead, a weak correlation is found with the length of the modeled protein: larger proteins required somewhat less accurate models to give successful molecular replacement. Overall, the results of this survey suggest that de novo models can phase diffraction data for approximately one sixth of proteins with sizes of 100 residues or less. However, for many of these cases, `de novo phasing with de novo models' requires significant investment of computational power, much greater than 103 CPU days per target. Improvements in conformational search methods will be necessary if molecular replacement with de novo models is to become a practical tool for targets without homology to previously solved protein structures. [source] The structure of the hexagonal crystal form of hen egg-white lysozymeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2006M. S. Weiss The three-dimensional structure of hen egg-white lysozyme (HEWL) in a hexagonal crystal form has been determined and refined to 1.46,Å resolution. This hexagonal crystal form crystallizes from a saturated sodium nitrate solution at pH 8.4. The crystals belong to space group P6122, with unit-cell parameters a = b = 85.64, c = 67.93,Å. A total of 165 water molecules, 16 nitrate ions and five sodium ions were located in the electron-density map. The hexagonal crystal form exhibits a higher solvent content and a higher degree of disorder than other crystal forms of lysozyme. The flexibility of the protein depends on the crystal packing, although some residue ranges are flexible in all native HEWL crystal forms. [source] Crystallization and preliminary crystallographic studies of MOMP (major outer membrane protein) from Campylobacter jejuniACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Jean Michel Bolla Campylobacter jejuni is the leading bacterial cause of human enteritis linked to ingestion of contaminated food or water. MOMP, the major outer membrane protein from these Gram-negative bacteria, belongs to the porin family. In order to determine the three-dimensional structure of this protein and to elucidate the underlying molecular mechanisms, the MOMP from C. jejuni strain 85H has been purified and crystallized by vapour diffusion. Two crystal forms were characterized for this membrane protein. X-ray diffraction data were collected to a resolution of 3.1,Å using a synchrotron-radiation source from the orthorhombic crystal form, which belonged to space group P21212 with unit-cell parameters a = 170.1, b = 101.9, c = 104.9,Å. With a trimer in the asymmetric unit, the solvent content is 64% (VM = 3.4,Å,Da,1). The other form exhibits trigonal symmetry (space group R3) with hexagonal unit-cell parameters a = b = 94.2, c = 161.2,Å, but diffracts X-rays poorly to about 4,Å with significant anisotropy. [source] Expression, crystallization and preliminary X-ray crystallographic studies of Klebsiella pneumoniae maltohexaose-producing ,-amylaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Mitsuru Momma A recombinant form of Klebsiella pneumoniae maltohexaose-producing ,-amylase has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293,K by the microbatch technique using 80,mM sodium/potassium phosphate buffer pH 6.2 containing 8% polyethylene glycol 3000, 4% polyethylene glycol 3350 and 40,mM sodium thiocyanate. Crystals of the overexpressed recombinant enzyme diffracted to better than 2.5,Å resolution at 95,K using a synchrotron-radiation source. The crystals belong to the primitive monoclinic space group P21, with unit-cell parameters a = 74.8, b = 107.6, c = 82.2,Å, , = 96.2°. Assuming the presence of two molecules per asymmetric unit, the VM value for the crystal was 2.3,Å3,Da,1, indicating a solvent content of 47%. [source] Crystallization and preliminary X-ray crystallographic analysis of a non-specific lipid-transfer protein with antipathogenic activity from Phaseolus mungoACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Shao-Yun Wang A 9,kDa non-specific lipid-transfer protein (nsLTP) from mung bean (Phaseolus mungo) seeds, displaying antifungal activity, antibacterial activity and lipid-transfer activity, was crystallized at 297,K using ammonium sulfate as a precipitant by means of the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to a resolution of 2.4,Å. The crystals are rhombohedral, belonging to space group P212121, with unit-cell parameters a = 38.671, b = 51.785, c = 55.925,Å. Assuming the presence of one molecule in the crystallographic asymmetric unit results in a Matthews coefficient (VM) of approximately 3.0,Å3,Da,1, corresponding to a solvent content of about 58%. [source] Crystallization and preliminary analysis of a water-forming NADH oxidase from Lactobacillus sanfranciscensisACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004George T. Lountos Single crystals have been obtained of NADH oxidase (Nox), a flavoenzyme cloned from Lactobacillus sanfranciscensis. The enzyme catalyzes the oxidation of two equivalents of NAD(P)H and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of NAD(P)H. The enzyme crystallizes in space group P212121, with unit-cell parameters a = 59.6, b = 92.6, c = 163.5,Å. The crystals diffract to 1.85,Å resolution using synchrotron radiation. Matthews coefficient calculations suggest the presence of two molecules per asymmetric unit (VM = 2.3,Å3,Da,1, 45.5% solvent content), which has been confirmed by the molecular-replacement solution using a search molecule derived from NADH peroxidase (PDB code 1f8w). [source] Cloning, expression, purification and crystallization of a transcriptional regulatory protein (Rv3291c) from Mycobacterium tuberculosis H37RvACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Tripti Shrivastava Rv3291c, the translational product of the Mycobacterium tuberculosisRv3291c gene, is an 18,kDa protein. It is a putative transcriptional regulatory protein belonging to the leucine-responsive regulatory protein/asparagine synthase C (Lrp/AsnC) family, which are proteins that have been identified in archaea and bacteria. Rv3291c probably plays a significant role during the persistent/latent phase of M. tuberculosis, as supported by its up-regulation several-fold during this stage. Orthorhombic crystals of recombinant Rv3291c have been grown from trisodium citrate dihydrate-buffered solutions containing monoammonium dihydrogen phosphate. Diffraction data extending to 2.7,Å have been collected from a single crystal with unit-cell parameters a = 99.6, b = 100.7, c = 100.6,Å. Assuming an octamer in the asymmetric unit results in a Matthews coefficient (VM) of 1.75,Å3,Da,1, corresponding to a solvent content of about 30%. [source] Purification, crystallization and preliminary X-ray crystallographic analysis of a cysteine-rich secretory protein (CRISP) from Naja atra venomACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Yu-Ling Wang Cysteine-rich secretory proteins (CRISPs) play an important role in the innate immune system and are transcriptionally regulated by androgens in several tissues. The proteins are mostly found in the epididymis and granules of mammals, whilst a number of snake venoms also contain CRISP-family proteins. The natrin protein from the venom of Naja atra (Taiwan cobra), which belongs to a family of CRISPs and has a cysteine-rich C-terminal amino-acid sequence, has been purified using a three-stage chromatography procedure and crystals suitable for X-ray analysis have been obtained using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.58,Å resolution using synchrotron radiation; the crystals belong to space group C2221, with unit-cell parameters a = 59.172, b = 65.038, c = 243.156,Å. There are two protein molecules in the asymmetric unit and the Matthews coefficient is estimated to be 2.35,Å3,Da,1, corresponding to a solvent content of 47.60%. [source] Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshiiACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Ryuya Fukunaga The leucyl-tRNA synthetase (LeuRS) from the archaeon Pyrococcus horikoshii was overexpressed in a C-terminally truncated form in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = b = 186.20, c = 91.43,Å, , = , = 90, , = 120°. The asymmetric unit contains one molecule of LeuRS, with a corresponding crystal volume per protein weight of 3.2,Å3,Da,1 and a solvent content of 60.7%. A data set diffracting to 2.2,Å resolution was collected from a single crystal at 100,K. Selenomethionine-substituted protein crystals were prepared in order to solve the structure by the SAD phasing method. [source] Crystallization and preliminary X-ray diffraction study of mammalian mitochondrial seryl-tRNA synthetaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Sarin Chimnaronk The mitochondrial seryl-tRNA synthetase (mt SerRS) from Bos taurus was overexpressed in Escherichia coli and crystallized using the sitting-drop vapour-diffusion method. Crystals grew in a very narrow range of conditions using PEG 8000 as precipitant at room temperature. An appropriate concentration of lithium sulfate was critical for crystal nucleation. Crystals diffracted well beyond a resolution of 1.6,Å and were found to belong to the orthorhombic space group C2221, with unit-cell parameters a = 79.89, b = 230.42, c = 135.60,Å. There is one dimer (Mr, 113,kDa) in the asymmetric unit, with a solvent content of 55%. Efforts to solve the phase problem by molecular replacement are under way. [source] Purification, crystallization, X-ray diffraction analysis and phasing of a Fab fragment of monoclonal neuroantibody ,D11 against nerve growth factorACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Sonia Covaceuszach The rat monoclonal neuroantibody ,D11 is a potent antagonist that prevents the binding of nerve growth factor (NGF) to its tyrosine kinase A receptor (TrkA) in a variety of systems, most notably in two in vivo systems linked to crucial pathological states, such as Alzheimer's disease and HIV infection. To provide further insights into the mechanism of action of this potentially therapeutic monoclonal antibody, structural studies of the antigen-binding fragment (Fab) of ,D11 were performed. ,D11 IgG2a immunoglobulin was obtained from hybridomas by in vitro tissue culture. The ,D11 Fab crystallizes in two crystal forms. Form I belongs to space group P1, with unit-cell parameters a = 42.7, b = 50.6, c = 102.7,Å, , = 82.0, , = 89.1, , = 86.0°. With two molecules in the asymmetric unit, VM is 2.3,Å3,Da,1 and the solvent content is 46%. A complete data set has been collected at 2.7,Å resolution on beamline XRD-1 (ELETTRA, Trieste, Italy). Form II belongs to space group C2, with unit-cell parameters a = 114.8, b = 69.4, c = 64.10,Å, , = 117.0°. With one molecule in the asymmetric unit, VM is 2.4,Å3,Da,1 and the solvent content is 48%. A complete data set has been collected at 1.7,Å resolution on beamline ID14-1 (ESRF, Grenoble, France). Phasing was successfully performed by Patterson search techniques and refinement of the structures is currently under way. Crystal forms I and II display a close-packing pattern. [source] Crystallization and preliminary X-ray crystallographic analysis of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosaACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2004Hye-Lee Kim The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an adenyl group from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. NaMN AT from Pseudomonas aeruginosa was overexpressed in Escherichia coli and crystallized at 291,K using 100,mM bis,Tris propane pH 7.0, 700,mM trisodium citrate and 15%(v/v) glycerol. X-ray diffraction data have been collected to 1.70,Å. The crystals are tetragonal, belonging to space group P4122 (or P4322), with unit-cell parameters a = b = 65.02, c = 109.80,Å. The presence of one monomer in the asymmetric unit gives a reasonable VM of 2.15,Å3,Da,1, with a solvent content of 42.7%. [source] Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Kazuaki Harata A triclinic crystal of hen egg-white lysozyme obtained from a D2O solution at 313,K was transformed into a new triclinic crystal by slow release of solvent under a temperature-regulated nitrogen-gas stream. The progress of the transition was monitored by X-ray diffraction. The transition started with the appearance of strong diffuse streaks. The diffraction spots gradually fused and faded with the emergence of diffraction from the new lattice; the scattering power of the crystal fell to a resolution of 1.5,Å from the initial 0.9,Å resolution. At the end of the transition, the diffuse streaks disappeared and the scattering power recovered to 1.1,Å resolution. The transformed crystal contained two independent molecules and the solvent content had decreased to 18% from the 32% solvent content of the native crystal. The structure was determined at 1.1,Å resolution and compared with the native structure refined at the same resolution. The backbone structures of the two molecules in the transformed crystal were superimposed on the native structure with root-mean-square deviations of 0.71 and 0.96,Å. A prominent structural difference was observed in the loop region of residues Ser60,Leu75. In the native crystal, a water molecule located at the centre of this helical loop forms hydrogen bonds to main-chain peptide groups. In the transformed crystal, this water molecule is replaced by a sodium ion with octahedral coordination that involves water molecules and a nitrate ion. The peptide group connecting Arg73 and Asn74 is rotated by 180° so that the CO group of Arg73 can coordinate to the sodium ion. The change in the X-ray diffraction pattern during the phase transition suggests that the transition proceeds at the microcrystal level. A mechanism is proposed for the crystal transformation. [source] Characterization, crystallization and preliminary X-ray analysis of bifunctional dihydrofolate reductase,thymidylate synthase from Plasmodium falciparumACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Penchit Chitnumsub The full-length pfdhfr-ts genes of the wild-type TM4/8.2 and the double mutant K1CB1 (C59R+S108N) from the genomic DNA of the corresponding Plasmodium falciparum parasite have been cloned into a modified pET(17b) plasmid and expressed in Escherichia coli BL21 (DE3) pLysS. Conditions for the expression and purification of the P. falciparum dihydrofolate reductase,thymidylate synthase (PfDHFR-TS) have been established that yield ,1,mg of the soluble active enzyme per litre of culture. The purified enzymes have been crystallized using a modified microbatch method with PEG 4000 as the primary precipitating agent. X-ray diffraction data were collected to 2.50 and 2.64,Å resolution under cryogenic conditions from single crystals of the two PfDHFR-TS proteins in complex with NADPH, dUMP and either Pyr30 or Pyr39. Preliminary X-ray analysis indicated that the crystals belong to the orthorhombic space group P212121, with two molecules per asymmetric unit and ,52% solvent content (VM, 2.6,Å3,Da,1). The use of a particular type of baby oil in the microbatch setup appeared to be beneficial to PfDHFR-TS crystallization and a preliminary comparison with another commonly used oil is described. [source] Crystallization and preliminary X-ray analysis of a novel Trichoderma reesei xylanase IV belonging to glycoside hydrolase family 5ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2004Tarja Parkkinen Xylanase IV (XYN IV) is a new recently characterized xylanase from Trichoderma reesei. It is able to degrade several different xylans, mainly producing xylose. XYN IV has been crystallized by the hanging-drop vapour-diffusion method, using PEG 6000 as a precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 86.3, b = 137.5, c = 196.1,Å, , = , = , = 90°. Assuming a molecular weight of 50.3,kDa, the VM values indicate there to be four XYN IV monomers in an asymmetric unit and the solvent content of the crystals to be 57%. Based on dynamic light-scattering measurements, XYN IV is a dimer in solution. A native data set to 2.8,Å resolution has been collected at a home laboratory and a data set to 2.2,Å resolution has been collected using synchrotron radiation. [source] Crystallization and preliminary X-ray crystallographic analysis of the RecR protein from Deinococcus radiodurans, a member of the RecFOR DNA-repair pathwayACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004Byung Il Lee The RecR protein plays a key role in the RecFOR pathway of recombination, which is necessary for the repair of ssDNA gaps. RecR from Deinococcus radiodurans has been overexpressed in Escherichia coli and crystallized at 297,K using polyethylene glycol 1000 as a precipitant. X-ray diffraction data to 2.90,Å resolution have been collected at 100,K using Cu,K, X-rays from a mercury-soaked crystal. The crystal belongs to space group C2221, with unit-cell parameters a = 106.96, b = 122.25, c = 156.01,Å. The asymmetric unit contains four monomers of RecR, with a crystal volume per protein weight (VM) of 2.57,Å3,Da,1 and a solvent content of 51.0%. [source] Expression, crystallization and preliminary X-ray crystallographic studies of Arthrobacter globiformis inulin fructotransferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Mitsuru Momma A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293,K by the hanging-drop vapour-diffusion technique using 0.1,M Na HEPES pH 7.5 buffer containing 1.5,M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5,Å at 100,K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82,Å in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the VM value for the crystal was 2.15,Å3,Da,1, indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58,Å, , = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit. [source] Crystallization and preliminary X-ray analysis of the glycogen synthase from Pyrococcus abyssiACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Cristina Horcajada Glycogen synthase catalyzes the transfer of glucosyl residues from ADP- or UDP-glucose to the non-reducing end of a growing ,-1,4-glucan chain. To date, no crystallographic structure of an animal/fungal glycogen synthase (family 3 of the glycosyl transferases) or a bacterial/plant glycogen/starch synthase (family 5) has been reported. This paper describes the recombinant expression, crystallization and preliminary X-ray analysis of the glycogen synthase from the hyperthermophilic archaeon Pyrococcus abyssi, the smallest enzyme of the members of families 3 and 5 of the glycosyl transferases. Crystals from this protein and from its selenomethionyl variant were grown in 100,mM sodium citrate pH 5.6 containing 20% PEG and 20% dioxane by the hanging-drop vapour-diffusion method at 293,K. The crystals, which grew as thin needles, diffracted to 3.5,Å resolution and belong to space group C2, with unit-cell parameters a = 202, b = 73, c = 149,Å, , = 131°. The crystallographic and biochemical data are consistent with either a dimer or a tetramer in the crystal asymmetric unit and a volume solvent content of 70 or 39%, respectively. [source] Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Valérie Campanacci The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive-stranded RNA virus (SARS-CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS-CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5,kbp in length, the largest of the known RNA viruses, and encode 20,30 mature proteins. The functions of many of these polypeptides, including the Nsp9,Nsp10 replicase-cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8,Å resolution and belong to space group P61/522, with unit-cell parameters a = b = 89.7, c = 136.7,Å. With two molecules in the asymmetric unit, the solvent content is 60% (VM = 3.1,Å3,Da,1). [source] Crystallization and preliminary X-ray data investigation of the bacterial enterocin A immunity protein at 1.65,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Bjørn Dalhus Crystals of the bacterial enterocin A immunity protein have been prepared by the hanging-drop vapour-diffusion technique at 293,K. The crystals diffract to better than 1.7,Å resolution and X-ray diffraction data to 1.65,Å have been collected at 110,K using synchrotron radiation. The enterocin A immunity protein crystals belong to the monoclinic crystal system, with unit-cell parameters a = 116.32, b = 42.35, c = 66.17,Å, , = 111.3°. The symmetry and systematic absences in the diffraction pattern are consistent with space group C2. The presence of two molecules in the asymmetric unit with a molecular weight of ,12.2,kDa gives a crystal volume per protein mass (VM) of ,3.1,Å3,Da,1 and a solvent content of ,60% by volume. [source] Crystallization and preliminary X-ray analysis of Yersinia pseudotuberculosis -derived mitogenACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Roberta Donadini Yersinia pseudotuberculosis -derived mitogen (YPM), a superantigen with no amino-acid sequence similarity to other known superantigens, has been crystallized by the sitting-drop vapour-diffusion method. The crystals belong to space group C2, with unit-cell parameters a = 138.67, b = 78.66, c = 32.91,Å, , = 91.97°. A native data set has been collected to a resolution of 1.8,Å using synchrotron radiation. Self-rotation function calculations suggest the presence of three molecules in the asymmetric unit, corresponding to a solvent content of 45%. [source] Crystallization and preliminary X-ray characterization of a novel calcium-binding protein AtCBL2 from Arabidopsis thalianaACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2003Masamichi Nagae A new family of calcineurin B-like calcium-binding proteins has recently been identified in Arabidopsis thaliana. AtCBL2, a member of this family, has been crystallized in the presence of calcium ions using polyethylene glycol as a precipitant at 293,K. The crystals belong to space group C2221, with unit-cell parameters a = 83.9, b = 118.1, c = 49.1,Å. The asymmetric unit contains one molecule, with a VM of 2.36,Å3,Da,1 and a solvent content of 48%. Native diffraction data to 2.1,Å resolution have been collected using synchrotron radiation at SPring-8. [source] Crystallization and preliminary crystallographic analysis of extracellular fragment X3 of YWK-II/APPH: a human sperm membrane protein related to the Alzheimer ,A4-amyloid precursor proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Wangjun Hu Crystals of extracellular fragment X3 of a human sperm membrane protein YWK-II/APPH have been grown at 291,K using 8% PEG 4000 as precipitant by the vapour-diffusion method. The diffraction pattern of the crystal extends to 2.9,Å resolution at 100,K using Cu,K, radiation in-house. The crystals belong to space group P21, with unit-cell parameters a = 46.0, b = 43.7, c = 90.2,Å, , = , = 90.0, , = 106.6°. Furthermore, a selenomethionine (SeMet) derivative of the protein was overexpressed in the same expression system and was purified in a reducing environment. The derivative crystals were obtained under similar conditions. Subsequently, a single-wavelength data set was collected to 2.38,Å resolution from the derivative crystal at ESRF. The crystals belong to space group P21, with unit-cell parameters a = 46.2, b = 44.0, c = 88.3,Å, , = , = 90.0, , = 103.6°. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (VM) of 2.8,Å3,Da,1 and a solvent content of 56.4% by volume. [source] Crystallization and preliminary X-ray analysis of candoxin, a novel reversible neurotoxin from the Malayan krait Bungarus candidusACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Palasingam Paaventhan Candoxin, a novel three-finger toxin from Bungarus candidus, is a reversible antagonist of muscle (,,,,) but a poorly reversible antagonist of neuronal ,7 nicotinic acetylcholine receptors. It has a molecular weight of 7344,Da, with 66 amino-acid residues including ten half-cystines. The fifth disulfide bridge is located at the tip of loop I (Cys6,Cys11) instead of in loop II as found in other ,-neurotoxins. Interestingly, candoxin lacks the segment cyclized by the fifth disulfide bridge at the tip of the middle loop of long-chain neurotoxins, which was reported to be critical for binding to ,7 receptors. As a first step to determining its three-dimensional structure, candoxin was crystallized by the hanging-drop vapour-diffusion technique in conditions around 1.5,M sodium chloride, 10%(v/v) ethanol. The crystals formed belonged to the hexagonal system, space group P6222, with unit-cell parameters a = 54.88, b = 54.88, c = 75.54,Å, , = , = 90, , = 120°, and diffract to a resolution of 1.80,Å. The crystallographic asymmetric unit contains one molecule of candoxin, with an estimated solvent content of 44.6%. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated. [source] Crystallization and preliminary X-ray diffraction studies of a mosquito-larvicidal toxin from Bacillus thuringiensis subsp. israelensisACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Panadda Boonserm The Cry4B ,-endotoxin from Bacillus thuringiensis subsp. israelensis is specifically toxic to mosquito larvae. For a better understanding of the mechanism of toxicity, chymotrypsin-activated Cry4B toxin (68,kDa) has been purified and crystallized in sodium bromide at neutral pH. The well formed crystals belong to the rhombohedral space group R32, with unit-cell parameters a = b = 185.82, c = 187.93,Å, and diffracted X-rays to 1.75,Å resolution. The asymmetric unit contains one toxin molecule and 74% solvent content, as shown by molecular replacement from a composite model of the homologous Cry3A and Cry1Aa. The purified protein and crystals both possessed mosquitocidal activity. [source] Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model biasACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003John F. Hunt Experimental phases could only be obtained to 4.4,Å resolution for crystals of the SecA translocation ATPase. Density modification of these phases exploiting the 65% solvent content of the crystal produced a map from which an approximate backbone model could be built for 80% of the structure. Combining the phases inferred from this partial model with the MIR phases and repeating the density modification produced an improved map from which a more complete backbone model could be built. However, this procedure converged before yielding a map, that allowed unambiguous sequence assignment for the majority of the protein molecule. In order to avoid the likely model bias associated with a speculative attempt at sequence assignment, a real-space cross-validation procedure was employed to facilitate completion of the crystal structure based on partial model phasing. The protein was partitioned into two disjoint sets of residues. Models in which the side chains were built for residues in one of the two sets were used for phase combination and density modification in order to produce improved electron density for interpretation of residues in the other set that had not been included in the model. Residues in the two sets were therefore omitted from the model in alternation except at sites where the side chain could be identified definitively based on phasing with the other set. This ping-pong cross-validation procedure allowed partial model phasing to be used to complete the crystal structure of SecA without being impeded by model bias. These results show that the structure of a large protein molecule can be solved with exclusively low-resolution experimental phase information based on intensive use of partial model phasing and density modification. Real-space cross-validation can be applied to reduce the risk of model bias associated with partial model phasing, streamlining this approach and expanding its range of applicability. [source] | ||||||||||