scholarly journals Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the N-terminal domain of serine glutamate repeat A (SgrA) protein fromEnterococcus faecium

2013 ◽  
Vol 69 (4) ◽  
pp. 441-444 ◽  
Author(s):  
Revathi Nagarajan ◽  
Antoni P. A. Hendrickx ◽  
Karthe Ponnuraj
Keyword(s):  
Ligand Binding ◽  
Hydrophobic Interaction Chromatography ◽  
Crystallographic Analysis ◽  
Host Cells ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Extracellular Matrix Molecule ◽  
Putative Ligand Binding

Serine glutamate repeat A (SgrA) protein is an LPxTG surface adhesin ofEnterococcus faeciumand is the first bacterial nidogen-binding protein identified to date. It has been suggested that it binds to human nidogen, the extracellular matrix molecule of basal lamina, and plays a key role in the invasion and colonization of eukaryotic host cells. SgrA28–288, having both a putative ligand-binding A domain and repetitive B domain, was expressed inEscherichia coliand purified using Ni-affinity and hydrophobic interaction chromatography. Further, the putative ligand-binding region, rSgrA28–153, was subcloned, overexpressed and purified in both native and selenomethionine-derivative forms. The native rSgrA28–153protein crystallized in the monoclinic space groupP21and diffracted to 3.3 Å resolution using an in-house X-ray source, with unit-cell parametersa= 35.84,b= 56.35,c= 60.20 Å, β = 106.5°.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of the ArsM arsenic(III)S-adenosylmethionine methyltransferase

2010 ◽  
Vol 66 (9) ◽  
pp. 1050-1052 ◽  
Author(s):  
Kavitha Marapakala ◽  
A. Abdul Ajees ◽  
Jie Qin ◽  
Banumathi Sankaran ◽  
Barry P. Rosen
Keyword(s):  
Crystallographic Analysis ◽  
Hazardous Substances ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Priority List ◽  
X Ray ◽  
Cell Parameters ◽  
Environmental Toxin

Arsenic is the most ubiquitous environmental toxin and carcinogen and consequently ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. A common biotransformation is methylation to monomethylated, dimethylated and trimethylated species. Methylation is catalyzed by the ArsM (or AS3MT) arsenic(III)S-adenosylmethionine methyltransferase, an enzyme (EC 2.1.1.137) that is found in members of every kingdom from bacteria to humans. ArsM from the thermophilic algaCyanidioschyzonsp. 5508 was expressed, purified and crystallized. Crystals were obtained by the hanging-drop vapor-diffusion method. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 84.85,b= 46.89,c= 100.35 Å, β = 114.25° and one molecule in the asymmetric unit. Diffraction data were collected at the Advanced Light Source and were processed to a resolution of 1.76 Å.

scholarly journals Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase fromMycobacterium smegmatis

2014 ◽  
Vol 70 (10) ◽  
pp. 1372-1375 ◽  
Author(s):  
Shanghua Fan ◽  
Defeng Li ◽  
Joy Fleming ◽  
Yuan Hong ◽  
Tao Chen ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Essential Enzyme ◽  
Mycobacterial Growth

7-Keto-8-aminopelargonic acid synthase (KAPA synthase; BioF) is an essential enzyme for mycobacterial growth that catalyses the first committed step in the biotin-synthesis pathway. It is a pyridoxal 5′-phosphate (PLP)-dependent enzyme and is a potential drug target. Here, the cloning, expression, purification and crystallization of KAPA synthase fromMycobacterium smegmatis(MsBioF) and the characterization of MsBioF crystals using X-ray diffraction are described. The crystals diffracted to 2.3 Å resolution and belonged to the monoclinic space groupP21, with unit-cell parametersa= 70.88,b= 91.68,c= 109.84 Å, β = 97.8°. According to the molecular weight of MsBioF, the unit-cell parameters and the self-rotation function map, four molecules are present in each asymmetric unit with aVMvalue of 2.06 Å3 Da−1and a solvent content of 40.20%.

scholarly journals The novel metallo-β-lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis

2018 ◽  
Vol 74 (10) ◽  
pp. 644-649 ◽  
Author(s):  
Kwang Seung Park ◽  
Myoung-Ki Hong ◽  
Jin Wan Jeon ◽  
Ji Hwan Kim ◽  
Jeong Ho Jeon ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metagenomic Library ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
The Novel ◽  
Unit Cell Parameters ◽  
Deep Sea Sediment ◽  
X Ray ◽  
Cell Parameters ◽  
Great Health

Metallo-β-lactamases (MBLs) are present in major Gram-negative pathogens and environmental species, and pose great health risks because of their ability to hydrolyze the β-lactam rings of antibiotics such as carbapenems. PNGM-1 was the first reported case of a subclass B3 MBL protein that was identified from a metagenomic library from deep-sea sediments that predate the antibiotic era. In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.10 and 2.30 Å resolution, respectively. Both the native and the selenomethionine-labelled PNGM-1 crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 122, b = 83, c = 163 Å, β = 110°. Matthews coefficient (V M) calculations suggested the presence of 6–10 molecules in the asymmetric unit, corresponding to a solvent content of ∼31–58%. Structure determination is currently in progress.

Pb-Sb zrudnění z Antimonitové žíly, důl Rudolf, Bohutín (Česká republika)

2021 ◽  
Vol 29 (2) ◽  
pp. 275-280
Author(s):  
Pavel Škácha ◽  
Jiří Sejkora
Keyword(s):  
Czech Republic ◽  
Chemical Composition ◽  
Empirical Formula ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Ore District ◽  
Archive Material

The Pb-Sb mineralization with dominant stibnite and plagionite and associated semseyite and zinkenite was found in an archive material collected at the Antimonitová vein, Bohutín, Březové Hory ore district (Czech Republic). Plagionite forms subhedral aggregates up to 1 mm in size. The unit-cell parameters of plagionite for monoclinic space group C2/c refined from the X-ray powder data are: a 13.4890(17), b 11.8670(14), c 19.997(2) Å, β 107.199(8)° and V 3057.9(6) Å3. Its chemical composition (average of 26 analyses, based on 30 apfu) corresponds to the empirical formula Pb5.02Sb8.15S16.82. Associated zinkenite is forming subhedral crystals up to 1 mm in size. Its empirical formula can be expressed as (Cu0.25Ag0.02Fe0.01)Σ0.28Pb9.22Sb22.19S41.31 (average of 26 analyses, based on 73 apfu). Semseyite aggregates have the empirical formula (Pb8.72Fe0.14)8.86Sb8.42S20.73 (average of 11 analyses, based on 38 apfu).

scholarly journals A putative siderophore-interacting protein from the marine bacteriumShewanella frigidimarinaNCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

2016 ◽  
Vol 72 (9) ◽  
pp. 667-671 ◽  
Author(s):  
Inês B. Trindade ◽  
Bruno M. Fonseca ◽  
Pedro M. Matias ◽  
Ricardo O. Louro ◽  
Elin Moe
Keyword(s):  
Iron Acquisition ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Interacting Protein ◽  
X Ray ◽  
Cell Parameters ◽  
Unit Structure ◽  
Shewanella Frigidimarina

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacteriumShewanella frigidimarinaNCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space groupP21, with unit-cell parametersa= 48.04,b= 78.31,c= 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

Crystal and X-Ray Powder Data for a New Organic Diphosphate [NH3(CH2)2NH3]2·P207

1991 ◽  
Vol 6 (4) ◽  
pp. 228-230
Author(s):  
Slaheddine Kamoun
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Metathesis Reaction ◽  
Chemical Preparation ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters

AbstractWith the help of Boulle's metathesis reaction, we have succeeded in preparing the compound [NH3(CH2)2NH3]2·P207. We describe its chemical preparation and main crystallographic features. The bis(ethylenediammonium) diphosphate salt is monoclinic, space group C2/c, with Z = 4. Unit cell parameters and powder diffraction data for this salt are reported.

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 Crystallization and preliminary X-ray crystallographic analysis of human myotubularin-related protein 1

2015 ◽  
Vol 71 (3) ◽  
pp. 261-265 ◽  
Author(s):  
Seoung Min Bong ◽  
Seung Won Yang ◽  
Ji-Woong Choi ◽  
Seung Jun Kim ◽  
Byung Il Lee
Keyword(s):  
Escherichia Coli ◽  
Polyethylene Glycol ◽  
Synchrotron Radiation ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Related Protein ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters

Myotubularin-related protein 1 is a phosphatase that dephosphorylates phospholipids such as phosphatidylinositol 3-phosphate or phosphatidylinositol 3,5-bisphosphate. In this study, human MTMR1 was overexpressed inEscherichia coli, purified and crystallized at 277 K using polyethylene glycol 20 000 as a precipitant. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation. The crystals belonged to space groupP1, with unit-cell parametersa= 67.219,b= 96.587,c= 97.581 Å, α = 87.597, β = 86.072, γ = 77.327°. Assuming the presence of four molecules in the asymmetric unit, the calculated Matthews coefficient value was 2.61 Å3 Da−1and the corresponding solvent content was 52.9%.

A new BaCa(CO3)2 polymorph

2019 ◽  
Vol 75 (3) ◽  
pp. 291-300
Author(s):  
Dominik Spahr ◽  
Lkhamsuren Bayarjargal ◽  
Victor Vinograd ◽  
Rita Luchitskaia ◽  
Victor Milman ◽  
...  
Keyword(s):  
Density Functional ◽  
Rietveld Analysis ◽  
Radioactive Isotopes ◽  
Synthesis Product ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Functional Theory ◽  
Model Calculations ◽  
X Ray ◽  
Cell Parameters

A new polymorph of the double carbonate BaCa(CO3)2, `a C2 phase', has been synthesized. Its structure has been obtained by density-functional-theory-based (DFT-based) model calculations and has been refined by Rietveld analysis of X-ray powder diffraction data. The structure of the new polymorph differs significantly from those of the established polymorphs barytocalcite, paralstonite and alstonite. The unit-cell parameters of the new monoclinic (space group C2) compound are a = 6.6775 (5), b = 5.0982 (4), c = 4.1924 (3) Å, β = 109.259 (1)°. The new compound has been further characterized using Raman spectroscopy. This work shows that earlier studies have misidentified the products of an established synthesis route and that findings based on the incorrect identification of the synthesis product concerning the suitability of barytocalcite as a matrix for the retention of radioactive isotopes will need to be reconsidered.

scholarly journals Production, crystallization and preliminary crystallographic analysis ofAllochromatium vinosumthiosulfate dehydrogenase TsdA, an unusual acidophilicc-type cytochrome

2014 ◽  
Vol 70 (10) ◽  
pp. 1424-1427 ◽  
Author(s):  
José A. Brito ◽  
André Gutierres ◽  
Kevin Denkmann ◽  
Christiane Dahl ◽  
Margarida Archer
Keyword(s):  
Crystallographic Analysis ◽  
Sulfur Cycle ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Oxidative Condensation ◽  
Unit Cell Parameters ◽  
Allochromatium Vinosum ◽  
Data Set ◽  
Purple Sulfur Bacterium ◽  
Cell Parameters

The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacteriumAllochromatium vinosumwas recombinantly expressed inEscherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 79.2,b= 69.9,c= 57.9 Å, β = 129.3°, contained one monomer per asymmetric unit and diffracted to a resolution of 1.98 Å.

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