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.

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 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°.

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.

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.

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.

A first Mn member in the struvite morphotropic series, CsMn(H2O)6(PO4): hydrothermal synthesis, crystal structure and interconnections within the family of related phosphates

2018 ◽  
Vol 74 (8) ◽  
pp. 936-943
Author(s):  
Galina V. Kiriukhina ◽  
Olga V. Yakubovich ◽  
Ekaterina M. Kochetkova ◽  
Olga V. Dimitrova ◽  
Anatoliy S. Volkov
Keyword(s):  
Crystal Structure ◽  
Ionic Radius ◽  
The Novel ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Cell Parameters ◽  
Structural Relationships ◽  
The Family

Caesium manganese hexahydrate phosphate, CsMn(H2O)6(PO4), was synthesized under hydrothermal conditions. Its crystal structure was determined from single-crystal X-ray diffraction data. The novel phase crystallizes in the hexagonal space group P63 mc and represents the first manganese member in the struvite morphotropic series, AM(H2O)6(TO4). Its crystal structure is built from Mn(H2O)6 octahedra and PO4 tetrahedra linked into a framework via hydrogen bonding. The large Cs atoms are encapsulated in the framework cuboctahedral cavities. It is shown that the size of the A + ionic radius within the morphotropic series AM(H2O)6(XO4) results is certain types of crystal structures and affects the values of the unit-cell parameters. Structural relationships with Na(H2O)Mg(H2O)6(PO4) and the mineral hazenite, KNa(H2O)2Mg2(H2O)12(PO4)2, are discussed.

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.

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