scholarly journals Preliminary crystallographic studies of aSchistosoma mansoniantigen (Sm21.7) dynein light-chain (DLC) domain

2014 ◽  
Vol 70 (6) ◽  
pp. 803-807 ◽  
Author(s):  
M. A. F. Costa ◽  
F. T. G. Rodrigues ◽  
B. C. A. Chagas ◽  
C. M. F. Rezende ◽  
A. M. Goes ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Monomethyl Ether ◽  
Dynein Light Chain ◽  
X Ray Diffraction ◽  
Three Dimensional Model ◽  
Major Health Problem ◽  
X Ray ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Drug Of Choice

Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) fromSchistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed inEscherichia coliand the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space groupP6122, with similar unit-cell parametersa=b= 108.5,c= 55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS–PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine.

scholarly journals EwaldSphere: an interactive approach to teaching the Ewald sphere construction

2018 ◽  
Vol 51 (6) ◽  
pp. 1734-1738 ◽  
Author(s):  
Leonard J. Barbour
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Three Dimensional Model ◽  
Interactive Approach ◽  
X Ray ◽  
Cell Parameters ◽  
Area Detector ◽  
Ewald Sphere ◽  
Microsoft Windows

EwaldSphere is a Microsoft Windows computer program that superimposes the Ewald sphere construction onto a small-molecule single-crystal X-ray diffractometer. The main objective of the software is to facilitate teaching of the Ewald sphere construction by depicting our classical description of the X-ray diffraction process as a three-dimensional model that can be explored interactively. Several features of the program are also useful for introducing students to the operation of a diffractometer. EwaldSphere creates a virtual reciprocal lattice based on user-defined unit-cell parameters. The Ewald sphere construction is then rendered visible, and the user can explore the effects of changing various diffractometer parameters (e.g. X-ray wavelength and intensity, goniometer angles, and detector distance) on the resulting diffraction pattern as captured by a virtual area detector. Additional digital resources are provided, including a simple but comprehensive program manual, a PowerPoint presentation that introduces the essential concepts, and an Excel file to facilitate calculation of lattice dhk spacings (required for the presentation). The program and accompanying resources are provided free of charge, and there are no restrictions on their use.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals PicW2 fromPicea wilsonii: preparation, purification, crystallization and X-ray diffraction analysis

2018 ◽  
Vol 74 (6) ◽  
pp. 363-366 ◽  
Author(s):  
Bei Zhang ◽  
Gangxing Guo ◽  
Fang Lu ◽  
Ying Song ◽  
Yong Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Gel Filtration ◽  
Three Dimensional ◽  
Temperature Tolerance ◽  
Diffusion Method ◽  
Limiting Factor ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Low temperature is a major limiting factor for plant growth and development. Dehydrin proteins are generally induced in response to low-temperature stress. In previous research, a full-length dehydrin gene,PicW2, was isolated fromPicea wilsoniiand its expression was associated with hardiness to cold. In order to gain insight into the mechanism of low-temperature tolerance by studying its three-dimensional crystal structure, prokaryotically expressed PicW2 dehydrin protein was purified using chitosan-affinity chromatography and gel filtration, and crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 MHEPES pH 8.0, 25%(w/v) PEG 3350 using 4 mg ml−1protein solution at 289 K. X-ray diffraction data were collected from a crystal at 100 K to 2.82 Å resolution. The crystal belonged to space groupC121, with unit-cell parametersa= 121.55,b= 33.26,c= 73.39 Å, α = γ = 90.00, β = 109.01°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.87 Å3 Da−1and a solvent content of 57.20%. Owing to a lack of structures of homologous dehydrin proteins, molecular-replacement trials failed. Data collection for selenium derivatization of PicW2 and crystal structure determination is currently in progress.

The new P-chalcopyrite compound Cu2FeIn2Se5; synthesis, thermal analysis (DTA), and crystal structure analysis by X-ray powder diffraction (XRPD)

2021 ◽  
Vol 67 (1 Jan-Feb) ◽  
pp. 18
Author(s):  
G. E. Delgado ◽  
P. Grima-Gallardo ◽  
J. A. Aitken ◽  
A. Cárdenas ◽  
I. Brito
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Chalcopyrite Structure ◽  
Distribution Analysis ◽  
X Ray Diffraction ◽  
Quaternary Compound ◽  
X Ray ◽  
Cell Parameters

The Cu2FeIn2Se5 alloy, belonging to the system (CuInSe2)1-x(FeSe)x with x= ⅓, was synthesized by the melt and annealing technique. The differential thermal analysis (DTA) indicates that this compound melts at 1017 K. The crystal structure of this new quaternary compound was established using powder X-ray diffraction. Cation distribution analysis indicates that this material crystallizes in a P-chalcopyrite structure, space group P2c (Nº 112), with unit cell parameters a = 6.1852(2) Å, c = 12.3633(9) Å, V = 472.98(4) Å3. Cu2FeIn2Se5 is a new adamantane type compound derivative of the sphalerite structure, and consists of a three-dimensional arrangement of distorted CuSe4, FeSe4, and InSe4 tetrahedral connected by common faces.

Crystal structure of low-cristobalite-type Al0.5Ga0.5PO4: A combined Rietveld refinement of neutron and X-ray diffraction data

2005 ◽  
Vol 20 (3) ◽  
pp. 207-211 ◽  
Author(s):  
S. N. Achary ◽  
A. K. Tyagi ◽  
S. K. Kulshreshtha ◽  
O. D. Jayakumar ◽  
P. S. R. Krishna ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Tetrahedral Coordination ◽  
X Ray Diffraction ◽  
Rietveld Refinements ◽  
X Ray ◽  
Cell Parameters ◽  
Bond Lengths

The low-cristobalite-type modification of Al0.5Ga0.5PO4 is prepared by annealing the amorphous precipitate of stoichiometric phosphate at 1300 °C. The phase purity of the sample is ascertained by powder X-ray diffraction. The crystal structure is refined by Rietveld refinements of the neutron and X-ray diffraction data of the polycrystalline powder. This compound crystallizes in an orthorhombic lattice with unit cell parameters, a=7.0295(8), b=7.0132(8), and c=6.9187(4) Å, V=341.08(6) Å3, Z=4 (Space group C 2221, No. 20). The crystal structure analysis reveals the random distribution of the Al3+ and Ga3+ having tetrahedral coordination with typical M–O (M=Al3+:Ga3+) bond lengths as 1.74 Å. Similarly, the P5+ have tetrahedral coordination with typical P–O bond lengths 1.52–1.54 Å. The Mo4 and PO4 tetraheda are linked by common corners forming a three-dimensional framework lattice. The details of the crystal structure are presented in this paper.

scholarly journals pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of theEscherichia colitype I restriction-modification system EcoR124I

2016 ◽  
Vol 72 (9) ◽  
pp. 672-676 ◽  
Author(s):  
Pavel Grinkevich ◽  
Iuliia Iermak ◽  
Nicholas A. Luedtke ◽  
Jeroen R. Mesters ◽  
Rüdiger Ettrich ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Type I ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Modification System ◽  
X Ray ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Restriction Modification System ◽  
Restriction Modification

The HsdR subunit of the type I restriction-modification system EcoR124I is responsible for the translocation as well as the restriction activity of the whole complex consisting of the HsdR, HsdM and HsdS subunits, and while crystal structures are available for the wild type and several mutants, the C-terminal domain comprising approximately 150 residues was not resolved in any of these structures. Here, three fusion constructs with the GFP variant pHluorin developed to overexpress, purify and crystallize the C-terminal domain of HsdR are reported. The shortest of the three encompassed HsdR residues 887–1038 and yielded crystals that belonged to the orthorhombic space groupC2221, with unit-cell parametersa= 83.42,b= 176.58,c= 126.03 Å, α = β = γ = 90.00° and two molecules in the asymmetric unit (VM= 2.55 Å3 Da−1, solvent content 50.47%). X-ray diffraction data were collected to a resolution of 2.45 Å.

scholarly journals Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system inThermotoga maritima

2014 ◽  
Vol 70 (6) ◽  
pp. 738-741 ◽  
Author(s):  
Shigeru Sugiyama ◽  
Keiko Kashiwagi ◽  
Keisuke Kakinouchi ◽  
Hideyuki Tomitori ◽  
Ken Kanai ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Crystallographic Analysis ◽  
Uptake System ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Polyamine Uptake ◽  
Preferential Uptake

A membrane-associated ATPase, PotA, is a component of the spermidine-preferential uptake system in prokaryotes that plays an important role in normal cell growth by regulating the cellular polyamine concentration. No three-dimensional structures of membrane-associated ATPases in polyamine-uptake systems have been determined to date. Here, the crystallization and preliminary X-ray diffraction analysis of PotA fromThermotoga maritimaare reported. Diffraction data were collected and processed to 2.7 Å resolution from both native and selenomethionine-labelled crystals. Preliminary crystallographic analysis revealed that the crystals belonged to the hexagonal space groupP3112 (orP3212), with unit-cell parametersa=b= 88.9,c= 221.2 Å, α = 90, β = 90, γ = 120°, indicating that a dimer was present in the asymmetric unit.

scholarly journals Brattforsite, Mn19(AsO3)12Cl2, a new arsenite mineral related to magnussonite, from Brattforsgruvan, Nordmark, Värmland, Sweden

2021 ◽  
Author(s):  
Dan Holtstam ◽  
Cristian Biagioni ◽  
Ulf Hålenius
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Type Specimen ◽  
Structural Topology ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Calculated Density ◽  
X Ray ◽  
Cell Parameters ◽  
Density Values

AbstractBrattforsite is an approved mineral (IMA2019-127), with ideal formula Mn19(AsO3)12Cl2. Associated minerals in the type specimen from the Brattfors mine, Nordmark (Värmland, Sweden) include jacobsite, alleghanyite, phlogopite, calcite and dolomite. Brattforsite, forming subhedral, mostly equant crystals up to 0.5 mm across, is orange to reddish-brown with a white streak, and translucent with a resinous to vitreous lustre. The fracture is uneven to subconchoidal, and no cleavage is observed. It is very weakly pleochroic in yellow, optically biaxial (–) with 2V = 44(5)° and has calculated mean refractive index of 1.981. Measured and calculated density values are 4.49(1) and 4.54(1) g·cm− 3, respectively. Chemical analyses yields (in wt%): MgO 0.62, CaO 1.26, MnO 48.66, FeO 0.13, As2O3 46.72, Cl 2.61, H2Ocalc 0.07, O ≡ Cl –0.59, sum 99.49, corresponding to the empirical formula (Mn17.67Ca0.58Mg0.40Fe0.05)∑18.70As12.17O35.90Cl1.90(OH)0.20, based on 38 (O + Cl + OH) atoms per formula unit. The five strongest Bragg peaks in the powder X-ray diffraction pattern are [d (Å), I (%), (hkl)]: 2.843,100, ($$ \overline{4} $$ 4 - 44); 2.828, 99, (444); 1.731, 32, (880); 2.448, 28, (800); 1.739, 25, (088). Brattforsite is monoclinic and pseudotetragonal, space group I2/a, with unit-cell parameters a = 19.5806(7), b = 19.5763(7), c = 19.7595(7) Å, β = 90.393(3)°, V = 7573.9(5) Å3 and Z = 8. The crystal structure was solved and refined to an R1 index of 3.4 % for 7445 reflections [Fo > 4σ(Fo)]. Brattforsite has the same overall structural topology as magnussonite (i.e., the species can be considered as homeotypic), but with 12 independent tetrahedrally coordinated As sites and 21 Mn sites with varying (4–8) coordination. The Mn-centered polyhedra, bonded through edge- and face-sharing, give rise to a three-dimensional framework. The (AsO3)3− groups are bonded to this framework through corner- and edge-sharing. Spectroscopic measurements (optical absorption, Raman, FTIR) carried out support the interpretation of the compositional and structural data.

scholarly journals Crystallization and preliminary X-ray diffraction studies of the family 54 carbohydrate-binding module from laminarinase (β-1,3-glucanase) Lic16A ofClostridium thermocellum

2015 ◽  
Vol 71 (2) ◽  
pp. 217-220 ◽  
Author(s):  
Yury A. Kislitsyn ◽  
Valeriya R. Samygina ◽  
Igor A. Dvortsov ◽  
Nataliya A. Lunina ◽  
Inna P. Kuranova ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Family ◽  
Overexpression System

The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacteriumClostridium thermocellum(ctCBM54) are reported. Recombinant ctCBM54 was prepared using anEscherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space groupP6322, with unit-cell parametersa=b= 130.15,c= 131.05 Å. The three-dimensional structure of ctCBM54 will provide valuable information about the structure–function relation of the laminarinase Lic16A and will allow the exploitation of this binding module in biotechnological applications.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of theEscherichia colicommon pilus chaperone EcpB

2015 ◽  
Vol 71 (6) ◽  
pp. 676-679 ◽  
Author(s):  
James A. Garnett ◽  
Mamou Diallo ◽  
Steve J. Matthews
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Solid Surfaces ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Common ◽  
First Time

Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. InEscherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space groupP3121 orP3221, with unit-cell parametersa=b= 62.65,c= 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

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