scholarly journals Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites

2015 ◽  
Vol 71 (9) ◽  
pp. 1161-1168 ◽  
Author(s):  
Christopher T. Jurgenson ◽  
Thomas D. Pollard
Keyword(s):  
Binding Site ◽  
Structural Information ◽  
Unit Cell ◽  
Molecular Structures ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
New Space

Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space groupP212121contained one complex per asymmetric unit, with unit-cell parametersa= 105.48,b= 156.71,c= 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space groupP41contained two complexes per asymmetric unit, with unit-cell parametersa=b= 149.93,c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.

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.

scholarly journals Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2)

1999 ◽  
Vol 55 (8) ◽  
pp. 1459-1461 ◽  
Author(s):  
Núria Verdaguer ◽  
Thomas C. Marlovits ◽  
Jerónimo Bravo ◽  
David I. Stuart ◽  
Dieter Blaas ◽  
...  
Keyword(s):  
Potassium Phosphate ◽  
Attachment Site ◽  
Unit Cell ◽  
Human Rhinovirus ◽  
Intercellular Adhesion Molecule ◽  
Upper Respiratory Tract ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters

Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group P21, diffracted at least to 2.8 Å resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 Å resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 Å, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 Å, diffracted to high resolution (beyond 1.8 Å) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.

Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli

1999 ◽  
Vol 55 (7) ◽  
pp. 1368-1369 ◽  
Author(s):  
Nicholas C. Blackwell ◽  
Paul M. Cullis ◽  
Ronald A. Cooper ◽  
Tina Izard
Keyword(s):  
Escherichia Coli ◽  
Packing Density ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
K 12

2-Dehydro-3-deoxygalactarate (DDG) aldolase (E.C. 4.1.2.20) catalyzes the reversible aldol cleavage of DDG and 2-dehydro-3-deoxyglucarate to pyruvate and tartronic semialdehyde. Rhombohedral crystals of recombinant DDG aldolase from Escherichia coli K-12 were obtained. The crystals belong to space group R32 with unit-cell parameters a = 93 Å, α = 85°. The crystals diffract to beyond 1.8 Å resolution on a Cu Kα rotating-anode generator. The asymmetric unit is likely to contain two molecules, corresponding to a packing density of 1.34 Å3 Da−1.

scholarly journals Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17

2012 ◽  
Vol 68 (2) ◽  
pp. 166-171 ◽  
Author(s):  
Carmela Garcia-Doval ◽  
Mark J. van Raaij
Keyword(s):  
Amino Acids ◽  
Protein A ◽  
Anomalous Dispersion ◽  
Unit Cell ◽  
Bacteriophage T7 ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Mercury Derivative

Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371–553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space groupP212121(unit-cell parametersa= 61.2,b= 86.0,c= 118.4 Å) and space groupC2221(unit-cell parametersa= 68.3,b= 145.6,c= 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress.

scholarly journals Purification, crystallization and preliminary X-ray data collection of the N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 fromMus musculus

2014 ◽  
Vol 70 (5) ◽  
pp. 611-615
Author(s):  
Wentao Diao ◽  
Xue Yang ◽  
Hao Zhou
Keyword(s):  
Unit Cell ◽  
26S Proteasome ◽  
Regulatory Subunit ◽  
Atpase Domain ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

The protein 26S proteasome regulatory subunit p27 is one of the four chaperones that help in the assembly of the 19S regulatory particle (RP) of the 26S proteasome. In the present work, the N-terminus of p27 (residues 1–128) fromMus musculuswas cloned, expressed, purified and crystallized alone and in complex with the C-terminal ATPase domain of Rpt5 (residues 173–442). The crystals of p27(1–128)diffracted to 1.7 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 26.79,b= 30.39,c= 145.06 Å. Resolution-dependent Matthews coefficient probability analysis suggested the presence of only one molecule per asymmetric unit, with 40.5% solvent content and aVMvalue of 2.02 Å3 Da−1. The crystal of the p27(1–128)–Rpt5(173–442)complex diffracted to 4 Å resolution and belonged to space groupP222, with unit-cell parametersa= 75.93,b= 76.08,c= 336.85 Å. The presence of four heterodimers in the asymmetric unit with 53.2% solvent content and aVMvalue of 2.63 Å3 Da−1or five heterodimers in the asymmetric unit with 41.5% solvent content and aVMvalue of 2.10 Å3 Da−1is assumed.

scholarly journals Two crystal forms of a helix-rich fatty acid- and retinol-binding protein, Na-FAR-1, from the parasitic nematodeNecator americanus

2012 ◽  
Vol 68 (7) ◽  
pp. 835-838 ◽  
Author(s):  
Mads Gabrielsen ◽  
M. Florencia Rey-Burusco ◽  
Kate Griffiths ◽  
Andrew J. Roe ◽  
Alan Cooper ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Structural Information ◽  
Binding Protein ◽  
Crystal Form ◽  
Blood Feeding ◽  
Unit Cell ◽  
Retinol Binding Protein ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters

Na-FAR-1 is an unusual α-helix-rich fatty acid- and retinol-binding protein fromNecator americanus, a blood-feeding intestinal parasitic nematode of humans. It belongs to the FAR protein family, which is unique to nematodes; no structural information is available to date for FAR proteins from parasites. Crystals were obtained with two different morphologies that corresponded to different space groups. Crystal form 1 exhibited space groupP432 (unit-cell parametersa = b = c = 120.80 Å, α = β = γ = 90°) and diffracted to 2.5 Å resolution, whereas crystal form 2 exhibited space groupF23 (unit-cell parametersa = b = c = 240.38 Å, α = β = γ = 90°) and diffracted to 3.2 Å resolution. Crystal form 2 showed signs of significant twinning.

scholarly journals N-Acetyl-L-glutamate kinase from Escherichia coli: cloning of the gene, purification and crystallization of the recombinant enzyme and preliminary X-ray analysis of the free and ligand-bound forms

1999 ◽  
Vol 55 (7) ◽  
pp. 1350-1352 ◽  
Author(s):  
Fernando Gil ◽  
Santiago Ramón-Maiques ◽  
Alberto Marina ◽  
Ignacio Fita ◽  
Vicente Rubio
Keyword(s):  
Escherichia Coli ◽  
Specific Activity ◽  
High Specific Activity ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
E Coli ◽  
Carbamate Kinase

The gene for Escherichia coli N-acetyl-L-glutamate kinase (NAGK) was cloned in a plasmid and expressed in E. coli, allowing enzyme purification in three steps. NAGK exhibits high specific activity (1.1 µmol s−1 mg−1), lacks Met1 and forms dimers (shown by cross-linking). Crystals of unliganded NAGK diffract to 2 Å and belong to space group P6122 or its enantiomorph P6522 (unit-cell parameters a = b = 78.6, c = 278.0 Å) with two monomers in the asymmetric unit. Crystals of NAGK with acetylglutamate and the ATP analogue AMPPNP diffract to 1.8 Å and belong to space group C2221 (unit-cell parameters a = 60.0, b = 71.9, c = 107.4 Å), with one monomer in the asymmetric unit. NAGK crystallization will allow the determination of proposed structural similarities to carbamate kinase.

Crystallization of ClfA and ClfB fragments: the fibrinogen-binding surface proteins of Staphylococcus aureus

1999 ◽  
Vol 55 (2) ◽  
pp. 554-556 ◽  
Author(s):  
Champion C. S. Deivanayagam ◽  
Samuel Perkins ◽  
Sita Danthuluri ◽  
Rick T. Owens ◽  
Todd Bice ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Unit Cell ◽  
Surface Proteins ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
Space Group ◽  
Cell Parameters ◽  
Fibrinogen Binding

Recombinant constructs encoding the fibrinogen-binding domains of ClfA and ClfB from Staphylococcus aureus have been crystallized. ClfA was crystallized in the orthorhombic space group P212121 with unit-cell parameters a = 39.58, b = 81.39 and c = 112.65 Å. A complete data set was recorded to 2.1 Å resolution and had a Vm of 2.3 Å3 Da−1 with 46.5% solvent, suggesting one molecule per asymmetric unit. Co-crystals of ClfA with the 17 amino-acid C-terminal peptide of fibrinogen γ-chain diffracted to 2.1 Å resolution and had unit-cell parameters a = 39.11, b = 81.39 and c = 109.51 Å in the space group P212121. ClfB was crystallized in the tetragonal space group P41212 or P43212 with unit-cell parameters a = 96.31, b = 96.31 and c = 84.13 Å and diffracted to 2.45 Å resolution. The estimated Vm of 2.6 Å3 Da−1 with 53% solvent indicated one molecule in the asymmetric unit.

scholarly journals Production, biophysical characterization and crystallization ofPseudomonas putidaGraA and its complexes with GraT and thegraTAoperator

2017 ◽  
Vol 73 (8) ◽  
pp. 455-462 ◽  
Author(s):  
Ariel Talavera ◽  
Hedvig Tamman ◽  
Andres Ainelo ◽  
San Hadži ◽  
Abel Garcia-Pino ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Biophysical Characterization ◽  
Space Group ◽  
Cell Parameters ◽  
Complex Forms ◽  
Saxs Analysis

ThegraTAoperon fromPseudomonas putidaencodes a toxin–antitoxin module with an unusually moderate toxin. Here, the production, SAXS analysis and crystallization of the antitoxin GraA, the GraTA complex and the complex of GraA with a 33 bp operator fragment are reported. GraA forms a homodimer in solution and crystallizes in space groupP21, with unit-cell parametersa= 66.9,b = 48.9,c= 62.7 Å, β = 92.6°. The crystals are likely to contain two GraA dimers in the asymmetric unit and diffract to 1.9 Å resolution. The GraTA complex forms a heterotetramer in solution. Crystals of the GraTA complex diffracted to 2.2 Å resolution and are most likely to contain a single heterotetrameric GraTA complex in the asymmetric unit. They belong to space groupP41orP43, with unit-cell parametersa=b= 56.0,c= 128.2 Å. The GraA–operator complex consists of a 33 bp operator region that binds two GraA dimers. It crystallizes in space groupP31orP32, with unit-cell parametersa=b= 105.6,c= 149.9 Å. These crystals diffract to 3.8 Å resolution.

scholarly journals Synthesis of Enaminones-Based Benzo[d]imidazole Scaffold: Characterization and Molecular Insight Structure

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 955
Author(s):  
Saeed Alshahrani ◽  
Saied M. Soliman ◽  
Abdullah Saleh Alamary ◽  
Abdullah Mohammed Al-Majid ◽  
Matti Haukka ◽  
...  
Keyword(s):  
Unit Cell ◽  
Imidazole Derivative ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Crystal ◽  
One Pot ◽  
Dimethylformamide Dimethylacetal ◽  
Space Group ◽  
Cell Parameters

(E)-1-(1H-Benzo[d]imidazol-2-yl)-3-(dimethylamino)prop-2-en-1-one 2 was synthesized by one-pot synthesis protocol of 2-acetyl benzo[d]imidazole with dimethylformamide dimethylacetal (DMF-DMA) in xylene at 140 °C for 8 h. Reaction of enaminone derivative 1 with acetylacetone in the presence of AcOH/NH4OAc under reflux afforded the cyclized pyridino-benzo[d]imidazole derivative 3. The latter compound was converted into the corresponding β-enaminone 4 with DMF-DMA. The single crystal X-ray diffraction technique eventually confirmed the assigned chemical structure of the N-alkyl-β-enaminone 2 and pyridino-benzo[d]imidazole derivative 3. N-alkyl-β-enaminone 2 crystallized in the monoclinic space group P21/n with unit cell parameters of a = 9.8953(3) Å, b = 5.7545(2) Å, c = 21.7891(7) Å, and β =100.627(2)°, and with one molecule per asymmetric unit. On the other hand, compound 3 crystallized in the orthorhombic crystal system and space group P212121 with unit cell parameters of a = 6.82950(10) Å, b = 8.00540(10) Å, c = 22.4779(2) Å, and also with one molecule per asymmetric unit. Based on Hirshfeld analysis, the H...H (51.3%), O...H (10.0%), N...H (10.3%), and C...H (27.6%) contacts in 2 and the H...H (46.8%), O...H (9.9%), N...H (13.0%), and C...H (21.6%) in addition to the C…C (6.7%) interactions in 3 are the most important towards crystal stability via molecular packing. The main difference is the presence of π–π interaction among the molecular units of 3 but not in 2. The calculated 1H and 13C NMR chemical shifts showed good agreements with experimental data. Electronic properties and reactivity parameters of both compounds are also calculated and compared.

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