scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase fromAspergillus niger

2014 ◽  
Vol 70 (11) ◽  
pp. 1508-1512 ◽  
Author(s):  
Prem Prakash ◽  
Adhish S. Walvekar ◽  
Narayan S. Punekar ◽  
Prasenjit Bhaumik
Keyword(s):  
Glutamate Dehydrogenase ◽  
Model Building ◽  
Specific Activity ◽  
Structure Refinement ◽  
High Specific Activity ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Carbon And Nitrogen

Glutamate dehydrogenase (GDH) catalyzes the NAD-dependent or NADP-dependent oxidative deamination of L-glutamate to 2-oxoglutarate and ammonia. This important reversible reaction establishes the link between carbon and nitrogen metabolism. In this study,Aspergillus nigerNADP-GDH (AnGDH) has been overexpressed and purified. Purified AnGDH, with a high specific activity of 631.1 units per milligram of protein, was crystallized and the crystal diffracted to 2.9 Å resolution using a home X-ray source. Preliminary analysis of the X-ray diffraction data showed that the crystal belonged to space groupR32, with unit-cell parametersa=b= 173.8,c= 241.5 Å, α = β = 90, γ = 120°. The crystals exhibited an unusually high solvent content (83.0%) and had only one molecule in the asymmetric unit. Initial phases were obtained by molecular replacement, and model building and structure refinement of AnGDH are in progress.

scholarly journals Purification and crystallographic analysis of a FAD-dependent halogenase fromStreptomycessp. JCM9888

2015 ◽  
Vol 71 (8) ◽  
pp. 972-976 ◽  
Author(s):  
Yanqun Zhao ◽  
Baohua Yan ◽  
Ting Yang ◽  
Jian Jiang ◽  
Heng Wei ◽  
...  
Keyword(s):  
Model Building ◽  
Structure Refinement ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Hexahistidine Tag ◽  
Crystallization Experiments

A new FAD (flavin adenine dinucleotide)-dependent halogenase HalY fromStreptomycessp. JCM9888 was reported to be involved in the regioselective halogenation of adenine. HalY is a variant B FAD-dependent halogenase that is most similar to the halogenase PltA involved in pyoluteorin biosynthesis. This study reports the overexpression and purification of HalY with an N-terminal hexahistidine tag, followed by crystallization experiments and X-ray crystallographic analysis. HalY was purified as a monomer in solution and crystallized to give X-ray diffraction to a resolution of 1.7 Å. The crystal belonged to the monoclinic space groupP21, with unit-cell parametersa= 41.4,b= 113.4,c= 47.6 Å, α = γ = 90, β = 107.4°, and contained one monomer of HalY in the asymmetric unit, with a calculated Matthews coefficient of 2.3 Å3 Da−1and a solvent content of 46%. The structure of the halogenase CndH was used as a search model in molecular replacement to obtain the initial model of HalY. Manual model building and structure refinement of HalY are in progress.

scholarly journals Preliminary X-ray diffraction analysis of a thermophilic β-1,3–1,4-glucanase fromClostridium thermocellum

2014 ◽  
Vol 70 (7) ◽  
pp. 946-948 ◽  
Author(s):  
Lilan Zhang ◽  
Puya Zhao ◽  
Chun-Chi Chen ◽  
Chun-Hsiang Huang ◽  
Tzu-Ping Ko ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Specific Activity ◽  
High Specific Activity ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Glycosidic Bonds ◽  
Hydrolysis Of

β-1,3–1,4-Glucanases catalyze the specific hydrolysis of internal β-1,4-glycosidic bonds adjacent to the 3-O-substituted glucose residues in mixed-linked β-glucans. The thermophilic glycoside hydrolase CtGlu16A fromClostridium thermocellumexhibits superior thermal profiles, high specific activity and broad pH adaptability. Here, the catalytic domain of CtGlu16A was expressed inEscherichia coli, purified and crystallized in the trigonal space groupP3121, with unit-cell parametersa=b= 74.5,c= 182.9 Å, by the sitting-drop vapour-diffusion method and diffracted to 1.95 Å resolution. The crystal contains two protein molecules in an asymmetric unit. Further structural determination and refinement are in progress.

Crystallization and Preliminary X-ray Diffraction Analysis of Cold-Active β-Galactosidase from Arthrobacter sp. C2-2

2005 ◽  
Vol 70 (1) ◽  
pp. 124-132 ◽  
Author(s):  
Hana Petroková ◽  
Eva Vondráčková ◽  
Tereza Skálová ◽  
Jan Dohnálek ◽  
Petra Lipovová ◽  
...  
Keyword(s):  
Structure Refinement ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Psychrotrophic Bacteria ◽  
Cold Active

β-Galactosidase from psychrotrophic bacteria strainArthrobactersp. C2-2 catalyzes cleavage of β-D-galactosyl moieties from β-D-galactosides and is interesting for its activity at low temperatures. Various types of crystals with dimensions of up to 0.8 mm were obtained and X-ray diffraction data up to 1.9 Å were collected. The crystals belong to the monoclinic space groupP21with unit-cell parametersa= 140.1 Å,b= 205.7 Å,c= 140.5 Å and β = 102.3°. The enzyme (molecular weight of a monomer is 111 kDa) forms hexamers in the crystal structure (one hexamer per asymmetric unit). The phase problem was solved by molecular replacement. Structure refinement is in progress.

scholarly journals Crystallization and preliminary X-ray analysis of a highly stable novel SGNH hydrolase (Est24) fromSinorhizobium meliloti

2014 ◽  
Vol 70 (2) ◽  
pp. 193-195 ◽  
Author(s):  
Bum Han Ryu ◽  
Duy Duc Nguyen ◽  
Tri Duc Ngo ◽  
Changsuk Oh ◽  
Ramesh Pandian ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Structure Refinement ◽  
Ammonium Phosphate ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Replacement Solution ◽  
Hydrolysis Of ◽  
Hydrolase Family

The SGNH hydrolase family includes enzymes that catalyze the hydrolysis of a broad range of substrates. Here, the crystallization and preliminary X-ray crystallographic studies of a novel SGNH hydrolase (Est24) fromSinorhizobium melilotiwere performed. Recombinant Est24 protein containing an N-terminal His tag was expressed inEscherichia coliand purified to homogeneity. Est24 was then crystallized using a solution consisting of 0.2 Mammonium phosphate pH 4.6, 20% polyethylene glycol 3350. X-ray diffraction data were collected to a resolution of 1.45 Å with anRmergeof 9.4%. The Est24 crystals belonged to space groupC2, with unit-cell parametersa= 129.09,b = 88.63,c= 86.15 Å, α = 90.00, β = 114.30, γ = 90.00°. A molecular-replacement solution was obtained using the crystal structure ofMycobacterium smegmatisarylesterase as a template and structure refinement of Est24 is in progress.

scholarly journals Crystallization and preliminary X-ray analysis of a novel type of lipolytic hydrolase fromBacillus licheniformis

2014 ◽  
Vol 70 (4) ◽  
pp. 473-475
Author(s):  
Hansol Ju ◽  
Ramesh Pandian ◽  
Kyungmin Kim ◽  
Kyeong Kyu Kim ◽  
T. Doohun Kim
Keyword(s):  
Structure Refinement ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 4000 ◽  
Replacement Solution ◽  
Increasing Demand ◽  
Identification And Characterization

With increasing demand in biotechnological applications, the identification and characterization of novel lipolytic enzymes are of great importance. The crystallization and preliminary X-ray crystallographic study of a novel type of hydrolase fromBacillus licheniformis(BL28) are described here. Recombinant BL28 protein containing a C-terminal His tag was overproduced inEscherichia coliand purified to homogeneity. BL28 was crystallized using 0.2 Mammonium acetate, 0.1 Msodium citrate tribasic dihydrate pH 5.6, 30%(w/v) PEG 4000 as a crystallizing solution. X-ray diffraction data were collected to a resolution of 1.67 Å with anRmergeof 5.8%. The BL28 crystals belonged to the tetragonal space groupP41212, with unit-cell parametersa=b= 57.89,c= 167.25 Å. A molecular-replacement solution was obtained and structure refinement of BL28 is in progress.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of a hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) fromCoffea canephorainvolved in chlorogenic acid biosynthesis

2012 ◽  
Vol 68 (7) ◽  
pp. 824-828 ◽  
Author(s):  
Laura A. Lallemand ◽  
James G. McCarthy ◽  
Sean McSweeney ◽  
Andrew A. McCarthy
Keyword(s):  
Structural Data ◽  
Coffea Canephora ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Key Enzyme ◽  
Substrate Specifities ◽  
Drop Technique ◽  
Better Than

Chlorogenic acids (CGAs) are a group of soluble phenolic compounds that are produced by a variety of plants, includingCoffea canephora(robusta coffee). The last step in CGA biosynthesis is generally catalysed by a specific hydroxycinnamoyl-CoA quinate hydroxycinnamoyltransferase (HQT), but it can also be catalysed by the more widely distributed hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT). Here, the cloning and overexpression of HCT fromC. canephorainEscherichia colias well as its purification and crystallization are presented. Crystals were obtained by the sitting-drop technique at 293 K and X-ray diffraction data were collected on the microfocus beamline ID23-2 at the ESRF. The HCT crystals diffracted to better than 3.0 Å resolution, belonged to space groupP42212 with unit-cell parametersa=b= 116.1,c= 158.9 Å and contained two molecules in the asymmetric unit. The structure was solved by molecular replacement and is currently under refinement. Such structural data are needed to decipher the molecular basis of the substrate specifities of this key enzyme, which belongs to the large plant acyl-CoA-dependent BAHD acyltransferase superfamily.

scholarly journals Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis

2015 ◽  
Vol 71 (4) ◽  
pp. 466-470 ◽  
Author(s):  
Ruyi Ding ◽  
Cui Xu ◽  
Xu Chen ◽  
Mengyun Bao ◽  
Xiaoting Qiu
Keyword(s):  
Diffraction Analysis ◽  
Biosynthetic Pathway ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Antithrombotic Activity ◽  
X Ray ◽  
Cell Parameters ◽  
Maximum Resolution ◽  
Replacement Method ◽  
Molecular Replacement Method

The 2-carboxy-6-hydroxyoctahydroindole moiety is an essential residue for the antithrombotic activity of aeruginosins, which are a class of cyanobacteria-derived bioactive linear tetrapeptides. The biosynthetic pathway of the 2-carboxy-6-hydroxyoctahydroindole moiety has not yet been resolved. AerF was indicated to be involved in the biosynthesis of the 2-carboxy-6-hydroxyoctahydroindole moiety. This study reports the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosawith a C-terminal His6tag. The crystal diffracted to a maximum resolution of 1.38 Å and belonged to the tetragonal space groupP4322, with unit-cell parametersa=b= 101.581,c= 116.094 Å. The calculated Matthews coefficient and solvent content of the crystal were 2.47 Å3 Da−1and 50.32%, respectively. The initial model of the structure was obtained by the molecular-replacement method and refinement of the structure is in progress.

Arrheniusite-(Ce), CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11, a New Member of the Vicanite Group, from the Östanmossa Mine, Norberg, Sweden

2021 ◽  
Author(s):  
Dan Holtstam ◽  
Luca Bindi ◽  
Paola Bonazzi ◽  
Hans-Jürgen Förster ◽  
Ulf B. Andersson
Keyword(s):  
Structure Refinement ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Calculated Density ◽  
Epma Data ◽  
X Ray ◽  
Cell Parameters ◽  
Greenish Yellow ◽  
The Ideal

ABSTRACT Arrheniusite-(Ce) is a new mineral (IMA 2019-086) from the Östanmossa mine, one of the Bastnäs-type deposits in the Bergslagen ore region, Sweden. It occurs in a metasomatic F-rich skarn, associated with dolomite, tremolite, talc, magnetite, calcite, pyrite, dollaseite-(Ce), parisite-(Ce), bastnäsite-(Ce), fluorbritholite-(Ce), and gadolinite-(Nd). Arrheniusite-(Ce) forms anhedral, greenish-yellow translucent grains, exceptionally up to 0.8 mm in diameter. It is optically uniaxial (–), with ω = 1.750(5), ε = 1.725(5), and non-pleochroic in thin section. The calculated density is 4.78(1) g/cm3. Arrheniusite-(Ce) is trigonal, space group R3m, with unit-cell parameters a = 10.8082(3) Å, c = 27.5196(9) Å, and V = 2784.07(14) Å3 for Z = 3. The crystal structure was refined from X-ray diffraction data to R1 = 3.85% for 2286 observed reflections [Fo > 4σ(Fo)]. The empirical formula for the fragment used for the structural study, based on EPMA data and results from the structure refinement, is: (Ca0.65As3+0.35)Σ1(Mg0.57Fe2+0.30As5+0.10Al0.03)Σ1[(Ce2.24Nd2.13La0.86Gd0.74Sm0.71Pr0.37)Σ7.05(Y2.76Dy0.26Er0.11Tb0.08Tm0.01Ho0.04Yb0.01)Σ3.27Ca4.14]Σ14.46(SiO4)3[(Si3.26B2.74)Σ6O17.31F0.69][(As5+0.65Si0.22P0.13)Σ1O4](B0.77O3)F11; the ideal formula obtained is CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11. Arrheniusite-(Ce) belongs to the vicanite group of minerals and is distinct from other isostructural members mainly by having a Mg-dominant, octahedrally coordinated site (M6); it can be considered a Mg-As analog to hundholmenite-(Y). The threefold coordinated T5 site is partly occupied by B, like in laptevite-(Ce) and vicanite-(Ce). The mineral name honors C.A. Arrhenius (1757–1824), a Swedish officer and chemist, who first discovered gadolinite-(Y) from the famous Ytterby pegmatite quarry.

scholarly journals MSMEG_6292, a Mycobacterium smegmatis RNA polymerase secondary channel-binding protein: purification, crystallization and X-ray diffraction analysis

2018 ◽  
Vol 74 (9) ◽  
pp. 543-548
Author(s):  
Abyson Joseph ◽  
Valakunja Nagaraja ◽  
Ramanathan Natesh
Keyword(s):  
Rna Polymerase ◽  
Mycobacterium Smegmatis ◽  
Transcriptional Activity ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Secondary Channel ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallization Method ◽  
Better Than

The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals. The crystals belonged to the trigonal space group P3121 (or its enantiomorph P3221), with unit-cell parameters a = b = 83.15, c = 107.07 Å, α = β = 90, γ = 120°. The crystals diffracted to better than 3.0 Å resolution. Molecular-replacement attempts did not yield any phasing models; hence, platinum derivatization was carried out with K2PtCl4 and derivative data were collected to 3.4 Å resolution.

scholarly journals Redetermination of Sr2PdO3 from single-crystal X-ray data

2019 ◽  
Vol 75 (1) ◽  
pp. 30-32
Author(s):  
Gohil S. Thakur ◽  
Hans Reuter ◽  
Claudia Felser ◽  
Martin Jansen
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Structure Type ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
Cell Parameters ◽  
Anisotropic Displacement Parameters

The crystal structure redetermination of Sr2PdO3 (distrontium palladium trioxide) was carried out using high-quality single-crystal X-ray data. The Sr2PdO3 structure has been described previously in at least three reports [Wasel-Nielen & Hoppe (1970). Z. Anorg. Allg. Chem. 375, 209–213; Muller & Roy (1971). Adv. Chem. Ser. 98, 28–38; Nagata et al. (2002). J. Alloys Compd. 346, 50–56], all based on powder X-ray diffraction data. The current structure refinement of Sr2PdO3, as compared to previous powder data refinements, leads to more precise cell parameters and fractional coordinates, together with anisotropic displacement parameters for all sites. The compound is confirmed to have the orthorhombic Sr2CuO3 structure type (space group Immm) as reported previously. The structure consists of infinite chains of corner-sharing PdO4 plaquettes interspersed by SrII atoms. A brief comparison of Sr2PdO3 with the related K2NiF4 structure type is given.

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