scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of GatD, a glutamine amidotransferase-like protein fromStaphylococcus aureuspeptidoglycan

2014 ◽  
Vol 70 (5) ◽  
pp. 632-635 ◽  
Author(s):  
Diana Vieira ◽  
Teresa A. Figueiredo ◽  
Anil Verma ◽  
Rita G. Sobral ◽  
Ana M. Ludovice ◽  
...  
Keyword(s):  
Sodium Acetate ◽  
Essential Feature ◽  
Calcium Acetate ◽  
Diffusion Method ◽  
Data Sets ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Amidation Reaction ◽  
Glutamine Amidotransferase

Amidation of peptidoglycan is an essential feature inStaphylococcus aureusthat is necessary for resistance to β-lactams and lysozyme. GatD, a 27 kDa type I glutamine amidotransferase-like protein, together with MurT ligase, catalyses the amidation reaction of the glutamic acid residues of the peptidoglycan ofS. aureus. The native and the selenomethionine-derivative proteins were crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol, sodium acetate and calcium acetate. The crystals obtained diffracted beyond 1.85 and 2.25 Å, respectively, and belonged to space groupP212121. X-ray diffraction data sets were collected at Diamond Light Source (on beamlines I02 and I04) and were used to obtain initial phases.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

Initiating a crystallographic study of UDP-galactopyranose mutase from Escherichia coli

1999 ◽  
Vol 55 (2) ◽  
pp. 399-402 ◽  
Author(s):  
Stephen A. McMahon ◽  
Gordon A. Leonard ◽  
Louise V. Buchanan ◽  
Marie-France Giraud ◽  
James H. Naismith
Keyword(s):  
Thin Plates ◽  
Diffusion Method ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Crystallographic Study ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Platinum Derivative

UDP-galactopyranose mutase, the enzyme responsible for the conversion of UDP-galactopyranose to UDP-galactofuranose, has been crystallized in a form suitable for X-ray diffraction studies. UDP-galactofuranose is a key component of mycobacterial cell walls. Crystals of both the native protein and a selenomethionine variant have been grown by the vapour-diffusion method in hanging drops, and diffract to beyond 3.0 Å using synchrotron radiation. Equilibration was against a solution of 20%(w/v) polyethylene glycol (4K), 12%(v/v) 2-propanol, 0.1 M HEPES pH 7.6 at 293.5 K. Crystals grow as thin plates of dimensions 0.4 × 0.2 × ∼0.02 mm. They are orthorhombic, space group P21, with unit-cell dimensions a = 71.12, b = 58.42, c = 96.38 Å, β = 96.38°. 92% (native) and 94% (selenomethionine) complete data sets have been recorded to 2.9 Å (R merge = 5.0%) and 3.0 Å (R merge = 6.9%), respectively. The Matthews coefficient is 2.35 Å3 Da−1 for a dimer in the asymmetric unit, the solvent content being 47%. Diffraction data have also been recorded on a putative platinum derivative to 3.5 Å.

scholarly journals Crystallization of uridine phosphorylase fromShewanella oneidensisMR-1 in the laboratory and under microgravity and preliminary X-ray diffraction analysis

2012 ◽  
Vol 68 (11) ◽  
pp. 1387-1389 ◽  
Author(s):  
Tatyana N. Safonova ◽  
Nadezhda N. Mordkovich ◽  
Konstantin M. Polyakov ◽  
Valentin A. Manuvera ◽  
Vladimir P. Veiko ◽  
...  
Keyword(s):  
Space Station ◽  
Shewanella Oneidensis ◽  
Free Form ◽  
Diffusion Method ◽  
Data Sets ◽  
Uridine Phosphorylase ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Key Enzyme

Uridine phosphorylase (UDP, EC 2.4.2.3), a key enzyme in the pyrimidine salvage pathway, catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The gene expression of UDP fromShewanella oneidensisMR-1 was performed in the recipient strainEscherichia coli. The UDP protein was crystallized on earth (in the free form and in complex with uridine as the substrate) by the hanging-drop vapour-diffusion method at 296 K and under microgravity conditions (in the free form) aboard the Russian Segment of the International Space Station by the capillary counter-diffusion method. The data sets were collected to a resolution of 1.9 Å from crystals of the free form grown on earth, 1.6 Å from crystals of the complex with uridine and 0.95 Å from crystals of the free form grown under microgravity. All crystals belong to the space groupP21and have similar unit-cell parameters. The crystal of uridine phosphorylase grown under microgravity diffracted to ultra-high resolution and gave high-quality X-ray diffraction data.

Technology of high quality protein crystals’ obtaining aboard the ISS at execution of joint Japanese–Russian experiments

2020 ◽  
pp. 5-25
Author(s):  
Koji INAKA ◽  
Saori ICHIMIZU ◽  
Izumi YOSHIZAKI ◽  
Kiyohito KIHIRA ◽  
Elena G. LAVRENKO ◽  
...  
Keyword(s):  
Drug Design ◽  
International Space Station ◽  
Space Station ◽  
Protein Crystals ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
High Quality ◽  
International Space ◽  
X Ray ◽  
High Quality Protein

A series of space experiments aboard the International Space Station (ISS) associated with high-quality Protein Crystal Growth (PCG) in microgravity conditions can be considered as a unique and one of the best examples of fruitful collaboration between Japanese and Russian scientists and engineers in space, which includes also other ISS International Partners. X-ray diffraction is still the most powerful tool to determine the protein three dimensional structure necessary for Structure based drug design (SBDD). The major purpose of the experiment is to grow high quality protein crystals in microgravity for X-ray diffraction on Earth. Within one and a half decade, Japan and Russia have established an efficient process over PCG in space to support latest developments over drug design and structural biology. One of the keys for success of the experiment lies in how precisely pre-launch preparations are made. Japanese party provides flight equipment for crystallization and ensures the required environment to support the experiment aboard of the ISS’s Kibo module, and also mainly takes part of the experiment ground support such as protein sample characterization, purification, crystallization screening, and solution optimization for microgravity experiment. Russian party is responsible for integration of the flight items equipped with proteins and precipitants on board Russian transportation space vehicles (Soyuz or Progress), for delivery them at the ISS, transfer to Kibo module, and returning the experiments’ results back on Earth aboard Soyuz manned capsule. Due to close cooperation of the parties and solid organizational structure, samples can be launched at the ISS every half a year if the ground preparation goes smoothly. The samples are crystallized using counter diffusion method at 20 degree C for 1–2.5 months. After samples return, the crystals are carefully taken out from the capillary, and frozen for X-ray diffraction at SPring8 facility in Japan. Extensive support of researchers from both countries is also a part of this process. The paper analyses details of the PCG experiment scheme, unique and reliable technology of its execution, and contains examples of the application. Key words: International Space Station, Protein crystals, Microgravity, International collaboration.

scholarly journals Optical, XPS and XRD Studies of Semiconducting Copper Sulfide Layers on a Polyamide Film

2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
Author(s):  
Valentina Krylova ◽  
Mindaugas Andrulevičius
Keyword(s):  
Photoelectron Spectroscopy ◽  
Copper Sulfide ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Xps Spectra ◽  
X Ray ◽  
Xrd Studies ◽  
Polyamide Film ◽  
Indirect Band Gap ◽  
Xrd Method

Copper sulfide layers were formed on polyamide PA 6 surface using the sorption-diffusion method. Polymer samples were immersed for 4 and 5 h in 0.15 mol⋅  solutions and acidified with HCl (0.1 mol⋅) at . After washing and drying, the samples were treated with Cu(I) salt solution. The samples were studied by UV/VIS, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) methods. All methods confirmed that on the surface of the polyamide film a layer of copper sulfide was formed. The copper sulfide layers are indirect band-gap semiconductors. The values of are 1.25 and 1.3 eV for 4 h and 5 h sulfured PA 6 respectively. Copper XPS spectra analyses showed Cu(I) bonds only in deeper layers of the formed film, while in sulfur XPS S 2p spectra dominating sulfide bonds were found after cleaning the surface with ions. It has been established by the XRD method that, beside , the layer contains as well. For PA 6 initially sulfured 4 h, grain size forchalcocite, , was  nm and fordjurleite, , it was 54.17 nm. The sheet resistance of the obtained layer varies from 6300 to 102 .

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the Csu pili CsuC–CsuA/B chaperone–major subunit pre-assembly complex fromAcinetobacter baumannii

2015 ◽  
Vol 71 (6) ◽  
pp. 770-774 ◽  
Author(s):  
Natalia Pakharukova ◽  
Minna Tuittila ◽  
Sari Paavilainen ◽  
Anton Zavialov
Keyword(s):  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Gram Negative ◽  
X Ray ◽  
Cell Parameters ◽  
Abiotic Surfaces ◽  
Vapour Diffusion ◽  
Fimbrial Adhesins

The attachment of many Gram-negative pathogens to biotic and abiotic surfaces is mediated by fimbrial adhesins, which are assembledviathe classical, alternative and archaic chaperone–usher (CU) pathways. The archaic CU fimbrial adhesins have the widest phylogenetic distribution, yet very little is known about their structure and mechanism of assembly. To elucidate the biogenesis of archaic CU systems, structural analysis of the Csu fimbriae, which are used byAcinetobacter baumanniito form stable biofilms and cause nosocomial infection, was focused on. The major fimbriae subunit CsuA/B complexed with the CsuC chaperone was purified from the periplasm ofEscherichia colicells co-expressing CsuA/B and CsuC, and the complex was crystallized in PEG 3350 solution using the hanging-drop vapour-diffusion method. Selenomethionine-labelled CsuC–CsuA/B complex was purified and crystallized under the same conditions. The crystals diffracted to 2.40 Å resolution and belonged to the hexagonal space groupP6422, with unit-cell parametersa=b= 94.71,c = 187.05 Å, α = β = 90, γ = 120°. Initial phases were derived from a single anomalous diffraction (SAD) experiment using the selenomethionine derivative.

A new model for packing of type-I collagen molecules in the native fibril

1981 ◽  
Vol 1 (10) ◽  
pp. 801-810 ◽  
Author(s):  
Karl A. Piez ◽  
Benes L. Trus
Keyword(s):  
Type I Collagen ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Equatorial Region ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Left Handed ◽  
Crystal Model ◽  
Collagen Molecules

A specific fibril model is presented consisting of bundles of five-stranded microfibrils, which are usually disordered (except axially) but under lateral compression become ordered. The features are as follows (where D = 234 residues or 67 nm): (1) D-staggered collagen molecules 4.5 D long in the helical microfibril have a left-handed supercoil with a pitch of 400–700 residues, but microfibrils need not have helical symmetry. (2) Straight-tilted 0.5-D overlap regions on a near-hexagonal lattice contribute the discrete x-ray diffraction reflections arising from lateral order, while the gap regions remain disordered. (3) The overlap regions are equivalent, but are crystallographically distinguished by systematic displacements from the near-hexagonal lattice. (4) The unit cell is the same as in a recently proposed three-dimensional crystal model, and calculated intensities in the equatorial region of the x-ray diffraction pattern agree with observed values.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

2012 ◽  
Vol 68 (7) ◽  
pp. 802-805 ◽  
Author(s):  
Lei Han ◽  
Zheng Liu ◽  
Xinqi Liu ◽  
Dewen Qiu
Keyword(s):  
Pathogenic Fungus ◽  
Sodium Formate ◽  
Diffusion Method ◽  
Effector Protein ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Dispersion Method ◽  
Data Set ◽  
X Ray ◽  
Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

The Effect of Different Methods to Pretreat Reed Pulp on the Crystallinity of Microcrystalline Cellulose

2014 ◽  
Vol 1056 ◽  
pp. 12-15 ◽  
Author(s):  
Wen Long Zhang ◽  
Wen Long Zhao ◽  
Ya Jie Dai
Keyword(s):  
Crystallite Size ◽  
Microcrystalline Cellulose ◽  
Average Crystallite Size ◽  
Comprehensive Analysis ◽  
Raw Material ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimethyl Acetamide ◽  
Crystal Type

Reed Pulp was Raw Material that Pretreated by Four Methods {ultrasonic, Microwave, N, N-Dimethyl Acetamide (DMAc) and Tetrahydrofuran (THF)}. Reed Microcrystalline Cellulose (MCC) was Prepared by the Dilute Hydrochloric Acid Hydrolysis from Pretreated Reed Pulp. the Influences of Pretreatment Methods on Crystalline Type, Crystallinity and Crystallite Size of MCC were Investigated by X-Ray Diffraction (XRD). the Results Showed that the Crystallinity of MCC with Four Pretreatment Methods was 68.45%, 62.28%, 63.21% and 69.56%, Respectively. the Average Crystallite Size of MCC Prepared by Hydrolysis after Pretreated by Dmac was the Largest. whereas, the Crystal Type of MCC was Not Changed, it was still the Cellulose Type I. Comprehensive Analysis Indicated that the Effects of MCC Prepared by Hydrolysis after Pretreated by Ultrasonic were the Best.

A Mn(II) Metal-Organic Framework Constructed from a Tetrahedral Silicon-Cored Ligand

2013 ◽  
Vol 275-277 ◽  
pp. 2367-2370
Author(s):  
Qing Yu Ma ◽  
Rui Fang Guan ◽  
Guo Zhong Li ◽  
Deng Xu Wang
Keyword(s):  
Single Crystal ◽  
Metal Organic Framework ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Slow Diffusion ◽  
Sheet Structure ◽  
Metal Organic ◽  
1D Chains ◽  
Organic Framework

A novel metal-organic framework, MnCl2(BIPS)2•2CH3OH•2H2O (1) were synthesized from MnCl2 and a tetrahedral silicon-cored ligand, Me2Si(p-C6H4-imdazol-1-yl)2 (BIPS) under the slow diffusion method. The structure was determined by single-crystal X-ray diffraction. Complex 1 is a 2D sheet structure constructed from 1D chains with 34-atom metallamacrocycles.

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