scholarly journals Expression, purification and crystallization of two endonuclease III enzymes fromDeinococcus radiodurans

2014 ◽  
Vol 70 (12) ◽  
pp. 1688-1692 ◽  
Author(s):  
Aili Sarre ◽  
Mats Ökvist ◽  
Tobias Klar ◽  
Elin Moe ◽  
Joanna Timmins
Keyword(s):  
Deinococcus Radiodurans ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Endonuclease Iii ◽  
Wide Range ◽  
Genes Encoding

Endonuclease III is a bifunctional DNA glycosylase that removes a wide range of oxidized bases in DNA.Deinococcus radioduransis an extreme radiation-resistant and desiccation-resistant bacterium and possesses three genes encoding endonuclease III enzymes in its genome: DR2438 (EndoIII-1), DR0289 (EndoIII-2) and DR0982 (EndoIII-3). Here, EndoIII-1 and an N-terminally truncated form of EndoIII-3 (EndoIII-3Δ76) have been expressed, purified and crystallized, and preliminary X-ray crystallographic analyses have been performed to 2.15 and 1.31 Å resolution, respectively. The EndoIII-1 crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 181.38,b= 38.56,c= 37.09 Å, β = 89.34° and one molecule per asymmetric unit. The EndoIII-3Δ76 crystals also belonged to the monoclinic space groupC2, but with unit-cell parametersa= 91.47,b= 40.53,c= 72.47 Å, β = 102.53° and one molecule per asymmetric unit. The EndoIII-1 structure was determined by molecular replacement, while the truncated EndoIII-3Δ76 structure was determined by single-wavelength anomalous dispersion phasing. Refinement of the structures is in progress.

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.

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 Purification, crystallization and preliminary crystallographic analysis of DR0248, an MNT–HEPN fused protein fromDeinococcus radiodurans

2015 ◽  
Vol 71 (1) ◽  
pp. 49-53
Author(s):  
Gaelle Pesce ◽  
Simone Pellegrino ◽  
Sean McSweeney ◽  
AnaMaria Goncalves ◽  
Daniele de Sanctis
Keyword(s):  
Deinococcus Radiodurans ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
Nucleotide Binding Domain ◽  
Unit Cell Parameters ◽  
Dodecyldimethylamine Oxide ◽  
Space Group ◽  
Cell Parameters ◽  
Nucleotidyl Transferase

DR0248 is a protein identified in theDeinococcus radiodurans(DR) genome that is predicted to encompass two domains: an N-terminal minimal nucleotidyl transferase domain (MNT) and a C-terminal higher eukaryotes and prokaryotes nucleotide-binding domain (HEPN). These two domains, usually encoded in two ORFs, have been suggested to play the role of a toxin–antitoxin (TA) system in prokaryotes. Recombinant DR0248 was overexpressed and purified fromEscherichia coliand diffraction-quality crystals were obtained in the presence of the detergent molecules dodecyldimethylamine oxide (DDAO) and octaethylene glycol monododecyl ether (C12E8), which were used as crystallization additives. Crystals grown with DDAO diffracted to a resolution of 2.24 Å and belonged to space groupC2221, with unit-cell parametersa= 98.4,b= 129.9,c= 59.2 Å. Crystals grown with C12E8 diffracted to a resolution of 1.83 Å and belonged to space groupP212121, with unit-cell parametersa= 51.6,b= 87.2,c= 108.2 Å. The structure was solved by multiwavelength anomalous dispersion from zinc bound to the protein using a single crystal obtained in the presence of DDAO.

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 preliminary X-ray diffraction studies of guanidinoacetate methyltransferase from rat liver

1999 ◽  
Vol 55 (11) ◽  
pp. 1928-1929 ◽  
Author(s):  
Junichi Komoto ◽  
Yafei Huang ◽  
Yongbo Hu ◽  
Yoshimi Takata ◽  
Kiyoshi Konishi ◽  
...  
Keyword(s):  
Rat Liver ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Guanidinoacetate methyltransferase is the enzyme which catalyzes the last step of creatine biosynthesis. The enzyme is found ubiquitously and in abundance in the livers of all vertebrates. Recombinant rat-liver guanidinoacetate methyltransferase has been crystallized with guanidinoacetate and S-adenosylhomocysteine. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 54.8, b = 162.5, c = 56.1 Å, β = 96.8 (1)° at 93 K, and typically diffract beyond 2.8 Å.

scholarly journals Pseudomalachit z lokality Zadné Breziny pri Gemerskej Polome (Slovenská republika)

2020 ◽  
Vol 28 (2) ◽  
pp. 290-294
Author(s):  
Martin Števko ◽  
Jiří Sejkora ◽  
Zdeněk Dolníček
Keyword(s):  
Wall Rock ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Native Copper ◽  
Space Group ◽  
Cell Parameters ◽  
Dark Green

A new occurrence of pseudomalachite was recently discovered at the Zadné Breziny copper occurrence near Gemerská Poloma, Rožňava Co., Košice Region, Slovakia. It forms dark green rich coatings and crusts, which consist of individual hemispherical aggregates up to 7 mm in size. Pseudostalactites up to 6 mm in size were also rarely observed. Pseudomalachite occurs in fractures and cavities of the quartz gangue or in fractures of the wall rock. It is associated with malachite, cuprite and native copper. The refined unit-cell parameters (for the monoclinic space group P21/c) are a 4.4805(5) Å, b 5.7504(6) Å, c 17.045(2) Å, β 91.12(1)° and V 439.06(6) Å3. Except of dominant contents of Cu and P only minor amounts of Al (up to 0.04 apfu), Fe (up to 0.02 apfu), As (up to 0.07 apfu) and S (up to 0.01 apfu) were detected in studied samples of pseudomalachite from the Zadné Breziny occurrence.

The crystal structure of Cu2GeSe3 and the structure-types of the I2-IV-VI3 family of semiconducting compounds

2021 ◽  
Vol 77 (1) ◽  
pp. 158-167
Author(s):  
Analio Dugarte-Dugarte ◽  
Nahum Ramírez Pineda ◽  
Luis Nieves ◽  
José Antonio Henao ◽  
Graciela Díaz de Delgado ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Initial Report ◽  
Space Group ◽  
Cell Parameters ◽  
Semiconducting Compounds ◽  
Bond Valence Model

Almost 50 years after the initial report, the crystal structure of Cu2GeSe3, a I2-IV-VI3 semiconductor, has been revised using modern single-crystal X-ray diffraction data. The structure of this material can be properly described in the monoclinic space group Cc (No. 9) with unit-cell parameters a = 6.7703 (4) Å, b = 11.8624 (5) Å, c = 6.7705 (4) Å, β = 108.512 (6)°, V = 515.62 (5) Å3, Z = 4, rather than in the orthorhombic space group Imm2 (No. 44) with unit-cell parameters a = 11.860 (3), b = 3.960 (1), c = 5.485 (2) Å, V = 257.61 Å3, Z = 2, as originally proposed [Parthé & Garín (1971). Monatsh. Chem. 102, 1197–1208]. Contrary to what was observed in the orthorhombic structure, the distortions of the tetrahedra in the monoclinic structure are consistent with the distortions expected from considerations derived from the bond valence model. A brief revision of the structures reported for the I2-IV-VI3 family of semiconducting compounds (I: Cu, Ag; IV: Si, Ge, Sn; and VI: S, Se, Te) is also presented.

Olivenite and cornwallite from the Podlipa copper deposit near Ľubietová, Slovakia

2021 ◽  
Vol 29 (2) ◽  
pp. 189-196
Author(s):  
Martin Števko ◽  
Jiří Sejkora ◽  
Zdeněk Dolníček
Keyword(s):  
Copper Deposit ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Chemical Zoning ◽  
Cell Parameters ◽  
P Content ◽  
Dark Green ◽  
Pale Green

An interesting occurrence of olivenite and cornwallite was recently discovered in cavities of quartz at the Podlipa copper deposit near Ľubietová, Slovakia. Olivenite occurs as olive to pale green sprays or radial aggregates consisting of individual acicular crystals up to 5 mm long. Its refined unit-cell parameters (for the monoclinic space group P21/n) are: a 8.6192(13) Å, b 8.2300(11) Å, c 5.9349(8) Å, α 90.055(12)° and V 420.99(7) Å3. Studied olivenite shows intense chemical zoning caused by strong variation of As and P contents. Most of the zones are corresponding to olivenite (with P content ranging between 0.02 to 0.39 apfu), but darker zones or domains of As-rich libethenite (with As content ranging between 0.18 to 0.24 apfu) were occasionally observed. Cornwallite forms dark green massive fillings between olivenite crystals or microcrystalline botryoidal crusts. The refined unit-cell parameters (for the monoclinic space group P21/c) of botryoidal cornwallite from the Podlipa deposit are: a 4.6112(2) Å, b 5.7698(3) Å, c 17.4167(11) Å, β 92.009(5)° and V 463.10(3) Å3. The two compositional types of cornwallite were distinguished. The first type is represented by relatively homogenous aggregates with only minor contents of P (from 0.04 to 0.22 apfu). The second type occurs as polycrystalline fillings with strong chemical zoning and has much more significant variation of As and P contents, representing solid-solution series between P-rich cornwallite (with 1.41 apfu of As and 0.59 apfu of P) and As-rich pseudomalachite (with 1.37 apfu of P and 0.63 apfu of As).

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