scholarly journals Purification, crystallization, crystallographic analysis and phasing of the CRISPR-associated protein Csm2 from Thermotoga maritima

2015 ◽  
Vol 71 (10) ◽  
pp. 1223-1227 ◽  
Author(s):  
Gloria Gallo ◽  
Gilles Augusto ◽  
Giulliana Rangel ◽  
André Zelanis ◽  
Marcelo A. Mori ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermotoga Maritima ◽  
Recombinant Expression ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Type Iiia ◽  
Associated Proteins ◽  
Sad Phasing ◽  
Interference Mechanism

The clusters of regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated proteins (Cas) system consists of an intriguing machinery of proteins that confer bacteria and archaea with immunity against phages and plasmids via an RNA-guided interference mechanism. Here, the cloning, recombinant expression in Escherichia coli BL21 (DE3), purification, crystallization and preliminary X-ray diffraction analysis of Csm2 from Thermotoga maritima are reported. Csm2 is thought to be a component of an important protein complex of the type IIIA CRISPR–Cas system, which is involved in the CRISPR–Cas RNA-guided interference pathway. The structure of Csm2 was solved via cadmium single-wavelength anomalous diffraction (Cd-SAD) phasing. Owing to its involvement in the CRISPR–Cas system, the crystal structure of this protein could be of importance in elucidating the mechanism of type IIIA CRISPR–Cas systems in bacteria and archaea.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase–RNA complex

2013 ◽  
Vol 69 (4) ◽  
pp. 421-424 ◽  
Author(s):  
Peter-Thomas Naumann ◽  
Charles T. Lauhon ◽  
Ralf Ficner
Keyword(s):  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dependent Modification ◽  
Rna Complex

The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI fromThermotoga maritimawas cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 102.9,b= 112.8,c= 132.8 Å.

scholarly journals SPICA: stereographic projection for interactive crystallographic analysis

2016 ◽  
Vol 49 (5) ◽  
pp. 1818-1826 ◽  
Author(s):  
X.-Z. Li
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Stereographic Projection ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Orientation Relationships ◽  
X Ray ◽  
Research Fields ◽  
Transmission Electron

In numerous research fields, especially the applications of electron and X-ray diffraction, stereographic projection represents a powerful tool for researchers. SPICA is a new computer program for stereographic projection in interactive crystallographic analysis, which inherits features from the previous JECP/SP and includes more functions for extensive crystallographic analysis. SPICA provides fully interactive options for users to plot stereograms of crystal directions and crystal planes, traces, and Kikuchi maps for an arbitrary crystal structure; it can be used to explore the orientation relationships between two crystalline phases with a composite stereogram; it is also used to predict the tilt angles of transmission electron microscopy double-tilt and rotation holders in electron diffraction experiments. In addition, various modules are provided for essential crystallographic calculations.

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 Crystallization and X-ray diffraction analysis of SpaE, a basal pilus protein from the gut-adaptedLactobacillus rhamnosusGG

2017 ◽  
Vol 73 (6) ◽  
pp. 321-327 ◽  
Author(s):  
Arjun K. Mishra ◽  
Abhin Kumar Megta ◽  
Airi Palva ◽  
Ingemar von Ossowski ◽  
Vengadesan Krishnan
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Molecular Mechanisms ◽  
Recombinant Expression ◽  
Lactobacillus Rhamnosus ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pilin Subunit ◽  
Sad Phasing

SpaE is the predicted basal pilin subunit in the sortase-dependent SpaFED pilus from the gut-adapted and commensalLactobacillus rhamnosusGG. Thus far, structural characterization of the cell-wall-anchoring basal pilins has remained difficult and has been limited to only a few examples from pathogenic genera and species. To gain a further structural understanding of the molecular mechanisms that are involved in the anchoring and assembly of sortase-dependent pili in less harmful bacteria,L. rhamnosusGG SpaE for crystallization was produced by recombinant expression inEscherichia coli. Although several attempts to crystallize the SpaE protein were unsuccessful, trigonal crystals that diffracted to a resolution of 3.1 Å were eventually produced using PEG 3350 as a precipitant and high protein concentrations. Further optimization with a combination of additives led to the generation of SpaE crystals in an orthorhombic form that diffracted to a higher resolution of 1.5 Å. To expedite structure determination by SAD phasing, selenium-substituted (orthorhombic) SpaE crystals were grown and X-ray diffraction data were collected to 1.8 Å resolution.

scholarly journals Expression, purification and X-ray crystallographic analysis of theHelicobacter pyloriblood group antigen-binding adhesin BabA

2014 ◽  
Vol 70 (12) ◽  
pp. 1631-1635 ◽  
Author(s):  
Suresh Subedi ◽  
Kristof Moonens ◽  
Ema Romão ◽  
Alvin Lo ◽  
Guy Vandenbussche ◽  
...  
Keyword(s):  
Recombinant Expression ◽  
Crystallographic Analysis ◽  
Antigen Binding ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Duodenal Ulcers ◽  
Antibiotic Resistant ◽  
X Ray ◽  
Cell Parameters ◽  
Resistant Strains

Helicobacter pyloriis a human pathogen that colonizes about 50% of the world's population, causing chronic gastritis, duodenal ulcers and even gastric cancer. A steady emergence of multiple antibiotic resistant strains poses an important public health threat and there is an urgent requirement for alternative therapeutics. The blood group antigen-binding adhesin BabA mediates the intimate attachment to the host mucosa and forms a major candidate for novel vaccine and drug development. Here, the recombinant expression and crystallization of a soluble BabA truncation (BabA25–460) corresponding to the predicted extracellular adhesin domain of the protein are reported. X-ray diffraction data for nanobody-stabilized BabA25–460were collected to 2.25 Å resolution from a crystal that belonged to space groupP21, with unit-cell parametersa= 50.96,b = 131.41,c= 123.40 Å, α = 90.0, β = 94.8, γ = 90.0°, and which was predicted to contain two BabA25–460–nanobody complexes per asymmetric unit.

Stereochemistry of α-Amino Oximes From the Monoterpene Hydrocarbons Car-3-ene, Limonene and α-Pinene

1992 ◽  
Vol 45 (6) ◽  
pp. 1077 ◽  
Author(s):  
AV Tkachev ◽  
AV Rukavishnikov ◽  
AM Chibiryaev ◽  
AY Denisov ◽  
YV Gatilov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Mechanics ◽  
High Field ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Molecular Mechanics Calculations ◽  
Space Group ◽  
X Ray ◽  
Monoterpene Hydrocarbons

The conformation and configuration of the α-amino oximes derived from the terpene hydrocarbons car-3-ene, limonene and α- pinene have been determined by n.m.r. spectroscopy (high-field 1H n.m.r., 13C n.m.r., INADEQUATE technique), molecular mechanics calculations and X-ray crystallographic analysis. The crystal structure of (lS,3S,6R)-3-dimethylamino-caran-4-one (E)-oxime has been determined by X-ray diffraction; crystals are orthorhombic, space group P 212121 with a 11.421(2), b 13.223(2), c 16.992(4) �, Z 8. Refinement on 1730 observed reflections measured with Cu K α radiation converged at R 0.053.

Crystal structure of an inclusion complex between chiral monoaza-15-crown-5 and S(–)-1-phenyl-ethyl ammonium percholorate

2003 ◽  
Vol 218 (5) ◽  
Author(s):  
Süheyla Özbey ◽  
F. B. Kaynak ◽  
M. Toğrul ◽  
N. Demirel ◽  
H. Hoşgören
Keyword(s):  
Crystal Structure ◽  
Inclusion Complex ◽  
Single Crystal ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
New Type

AbstractA new type of inclusion complex, S(–)-1 phenyl ethyl ammonium percholorate complex of R-(–)-2-ethyl - N - benzyl - 4, 7, 10, 13 - tetraoxa -1- azacyclopentadecane, has been prepared and studied by NMR, IR and single crystal X-ray diffraction techniques. The compound crystallizes in space group

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

scholarly journals High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

2019 ◽  
Vol 74 (4) ◽  
pp. 357-363
Author(s):  
Daniela Vitzthum ◽  
Hubert Huppertz
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
High Temperature ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Mixed Cation ◽  
High Pressure High Temperature ◽  
Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

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