Purification, crystallization and preliminary X-ray crystallographic analysis of a phospholipase A2 from Daboia russelli pulchella

1999 ◽  
Vol 55 (4) ◽  
pp. 925-926 ◽  
Author(s):  
Vikas Chandra ◽  
Akanksha Nagpal ◽  
A. Srinivasan ◽  
T. P. Singh
Keyword(s):  
Crystallographic Analysis ◽  
Diffusion Method ◽  
The Novel ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Sequence Identity ◽  
Class 1

Phospholipases are esterolytic enzymes which hydrolyze glycerophospholipids. The pharmacological efficiency of phospholipase A2 (PLA2) enzymes is reflected by their specificity towards a tissue or organ. The Russell's viper has been classified into two classes. Class 1 contains Viper russelli russelli, Viper russelli siamensis and Viper russelli formosensis, whereas class 2 contains Daboia russelli pulchella. The sequence identity between the PLA2s from these two classes is 47%. The novel PLA2 from Daboia russelli pulchella has been crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitating agent. Crystals belong to the orthorhombic space group C2221 with unit-cell parameters a = 77.01, b = 92.29, c = 76.90 Å and two molecules in the asymmetric unit. These crystals diffract to about 2.49 Å resolution using a rotating-anode source.

scholarly journals Crystallization and preliminary X-ray analysis of the hypothetical deaminase RPB_0146 fromRhodopseudomonas palustrisHaA2

2014 ◽  
Vol 70 (11) ◽  
pp. 1560-1562
Author(s):  
Guofang Zhang ◽  
Dan Yu ◽  
Guodong Yang ◽  
Hui Dong ◽  
Tongcun Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rhodopseudomonas Palustris ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion

RPB_0146, a putative deaminase fromRhodopseudomonas palustrisHaA2, was expressed inEscherichia coliBL21 (DE3) cells and purified using a His6tag by Ni2+-chelating affinity chromatography for X-ray crystallographic analysis. Diffraction-quality crystals were grown by the hanging-drop vapour-diffusion method at 289 K and diffracted to a resolution of 2.44 Å using a wavelength of 1.000 Å at the Photon Factory (KEK), Japan. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 66.26,b= 123.94,c= 155.95 Å.

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, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain

2014 ◽  
Vol 70 (10) ◽  
pp. 1414-1417 ◽  
Author(s):  
Seung Mi Lee ◽  
Hyun Ho Park
Keyword(s):  
Fruit Fly ◽  
Diffusion Method ◽  
Amino Acid Residues ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Protein Interaction

Drep2 is a novel nuclease from the fruit fly that might have a similar function in apoptosis to DFF40 and DFF45, which are primary players in apoptotic DNA fragmentation. Drep2 contains a conserved CIDE domain of ∼90 amino-acid residues that is involved in protein–protein interaction. In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3 Å. The crystals were found to belong to the orthorhombic space groupP212121, with unit-cell parametersa= 50.28,b= 88.70,c= 113.37 Å.

Crystallization and preliminary X-ray diffraction analysis of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

1999 ◽  
Vol 55 (6) ◽  
pp. 1231-1233 ◽  
Author(s):  
Ivana Smatanová ◽  
Yuji Nagata ◽  
L. Anders Svensson ◽  
Masamichi Takagi ◽  
Jaromír Marek
Keyword(s):  
Diffusion Method ◽  
Sphingomonas Paucimobilis ◽  
Asymmetric Unit ◽  
Haloalkane Dehalogenase ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

Haloalkane hydrolytic dehalogenase LinB from Sphingomonas paucimobilis UT26, an enzyme which releases chloride or bromide anion from n-halogenated alkanes and has a broad range of substrate specificity, was crystallized using the hanging-drop vapour-diffusion method at 278 K. The best crystals were obtained by microseeding with a precipitant containing 18–20%(w/v) PEG 6000, 0.2 M calcium acetate and 0.1 M Tris–HCl pH 8.9. The crystals diffract to at least 1.60 Å using synchrotron X-ray under cryogenic (100 K) conditions. They belong to the orthorhombic space group P21212 with unit-cell parameters a = 50.29, b = 71.70, c = 72.73 Å. The asymmetric unit contains one molecule of the enzyme.

scholarly journals Plant-specific DUF1110 protein fromOryza sativa: expression, purification and crystallization

2016 ◽  
Vol 72 (6) ◽  
pp. 480-484 ◽  
Author(s):  
Kenichi Harada ◽  
Eiki Yamashita ◽  
Kento Inoue ◽  
Koji Yamaguchi ◽  
Toshimichi Fujiwara ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Sequence Identity ◽  
Vapour Diffusion ◽  
Domain Of Unknown Function

The Os01T0156300 protein fromOryza sativahas been classified into the domain of unknown function (DUF) family DUF1110. DUF1110 family members exist in monocotyledons but not in dicotyledons, and share no sequence identity with proteins for which structures have been reported. In this study, the Os01T0156300 protein was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.84 Å resolution. The crystal belonged to space groupP21, with unit-cell parametersa= 89.9,b= 89.8,c= 107.1 Å, β = 106.6°. The asymmetric unit was estimated to contain 6–11 molecules.

scholarly journals Crystallization and preliminary X-ray study of biosynthetic alanine racemase fromPseudomonas aeruginosaPAO1

2014 ◽  
Vol 70 (12) ◽  
pp. 1616-1619 ◽  
Author(s):  
Honggang Zhou ◽  
Zhenzhen Li ◽  
Guofang Zhang ◽  
Shujing Xu ◽  
Zhaona Tang ◽  
...  
Keyword(s):  
Protein Concentration ◽  
Anion Exchange Chromatography ◽  
Crystallographic Analysis ◽  
Exchange Chromatography ◽  
Alanine Racemase ◽  
Diffusion Method ◽  
Hanging Drop ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

Biosynthetic alanine racemase (AlrPA) fromPseudomonas aeruginosaPAO1 carrying a His6tag was expressed inEscherichia coliBL21 (DE3) cells and purified by Ni2+-chelating affinity and anion-exchange chromatography for X-ray crystallographic analysis. Crystals were grown by the hanging-drop vapour-diffusion method at 289 K in a solution consisting of 4%(v/v) Tacsimate pH 5.0, 14%(w/v) polyethylene glycol 3350 with a protein concentration of 8 mg ml−1. The crystal diffracted to 2.76 Å resolution and belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 74.12,b= 76.97,c= 154.80 Å, α = β = γ = 90°.

scholarly journals Overexpression, crystallization and preliminary X-ray crystallographic analysis of hypothetical protein SAV0479 fromStaphylococcus aureusMu50

2013 ◽  
Vol 69 (4) ◽  
pp. 405-407
Author(s):  
Chinar Pathak ◽  
Sun-Bok Jang ◽  
Hookang Im ◽  
Hye-Jin Yoon ◽  
Bong-Jin Lee
Keyword(s):  
Hypothetical Protein ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Vancomycin Resistant ◽  
And Function

SAV0479, a hypothetical protein from the Mu50 strain of methicillin- and vancomycin-resistantStaphylococcus aureus, was selected for structure and function determination as part of a structural genomics project. Here, the cloning, overexpression, purification and crystallization of SAV0479 are reported. Crystals were obtained by the hanging-drop vapour-diffusion method and diffraction data were collected to a resolution of 2.8 Å. The crystals belonged to space groupP3121, with unit-cell parametersa=b= 81.48,c= 82.53 Å. Three monomers of SAV0479 are present in each asymmetric unit.

scholarly journals A thermostable and alkaline GDSL-motif esterase from Bacillus sp. K91: crystallization and X-ray crystallographic analysis

2018 ◽  
Vol 74 (2) ◽  
pp. 117-121 ◽  
Author(s):  
Junmei Ding ◽  
Hujie Zhu ◽  
Yujia Ye ◽  
Jie Li ◽  
Nanyu Han ◽  
...  
Keyword(s):  
Thermophilic Bacterium ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallization Solution ◽  
Gdsl Family

The esterase Est8 from the thermophilic bacterium Bacillus sp. K91 belongs to the GDSL family and is active on a variety of acetylated compounds, including 7-aminocephalosporanic acid. In contrast to other esterases of the GDSL family, the catalytic residues Asp182 and His185 were more pivotal for the catalytic activity of Est8 than the Ser11 residue. To better understand the biochemical and enzymatic properties of Est8, recombinant Est8 protein was purified and crystallized. Crystals of Est8 were obtained by the hanging-drop vapour-diffusion method using 2.0 M ammonium sulfate, 5%(v/v) 2-propanol as the crystallization solution. X-ray diffraction data were collected to a resolution of 2.30 Å with an R merge of 16.4% from a crystal belonging to space group P41212 or P43212, with unit-cell parameters a = b = 68.50, c = 79.57 Å.

Crystallization and preliminary X-ray crystallographic analysis of a vancomycin–N-acetyl-D-Ala-D-Ala complex

1999 ◽  
Vol 55 (2) ◽  
pp. 534-535 ◽  
Author(s):  
Deborah McPhail ◽  
Alan Cooper ◽  
Andy Freer
Keyword(s):  
Room Temperature ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
The Novel ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal Density

A vancomycin–N-acetyl-D-Ala-D-Ala complex has been crystallized by the sitting-drop vapour-diffusion method using imidazole maleic buffer at pH 7.6. The novel crystals obtained belong to the space group P6322 with unit-cell parameters a = b = 73.43 (1), c = 277.17 (4) Å, γ = 120°. The crystal density was determined as 1.106 g cm−3 which gives a supercell of 24 molecules (12 dimers) per asymmetric unit for an acceptable Matthews number and an estimated solvent content of 42%. Data were collected at room temperature to 2.8 Å.

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.

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