scholarly journals The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacteriumBartonella henselaestrain Houston-1 at 2.3 Å resolution

2016 ◽  
Vol 72 (12) ◽  
pp. 885-891 ◽  
Author(s):  
Ali R. Cala ◽  
Maria T. Nadeau ◽  
Jan Abendroth ◽  
Bart L. Staker ◽  
Alexandra R. Reers ◽  
...  
Keyword(s):  
Sodium Citrate ◽  
Bartonella Henselae ◽  
Three Dimensional ◽  
Structural Features ◽  
Cat Scratch Disease ◽  
X Ray Diffraction ◽  
Cell Parameters ◽  
Human Pathogenic Bacterium ◽  
Peg 4000 ◽  
Causative Bacterium

In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacteriumBartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mMsodium acetate, 100 mMsodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space groupP4322, with unit-cell parametersa= 109.38,b= 109.38,c= 176.95 Å.Rr.i.m.was 0.11,Rworkwas 0.177 andRfreewas 0.208. The three-dimensional structural features of the enzymes show that DapB fromB. henselaeis a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.

scholarly journals Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacteriumBartonella henselaestrain Houston-1 at 2.1 Å resolution

2016 ◽  
Vol 72 (1) ◽  
pp. 2-9 ◽  
Author(s):  
Kubra F. Naqvi ◽  
Bart L. Staker ◽  
Renwick C. J. Dobson ◽  
Dmitry Serbzhinskiy ◽  
Banumathi Sankaran ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Sodium Citrate ◽  
Bartonella Henselae ◽  
Cat Scratch Disease ◽  
Dihydrodipicolinate Synthase ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 4000 ◽  
Causative Bacterium

The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacteriumBartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mMsodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space groupP212121, with unit-cell parametersa= 79.96,b= 106.33,c= 136.25 Å. The finalRvalues wereRr.i.m.= 0.098,Rwork= 0.183,Rfree= 0.233.

scholarly journals Crystallization and preliminary X-ray analysis of the major peanut allergen Ara h 1 core region

2010 ◽  
Vol 66 (9) ◽  
pp. 1071-1073 ◽  
Author(s):  
Cerrone Cabanos ◽  
Hiroyuki Urabe ◽  
Taro Masuda ◽  
Mary Rose Tandang-Silvas ◽  
Shigeru Utsumi ◽  
...  
Keyword(s):  
Sodium Citrate ◽  
Three Dimensional ◽  
Core Region ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 400 ◽  
Ara H 1 ◽  
Peanut Allergens

Peanuts contain some of the most potent food allergens known to date. Ara h 1 is one of the three major peanut allergens. As a first step towards three-dimensional structure elucidation, recombinant Ara h 1 core region was cloned, expressed inEscherichia coliand purified to homogeneity. Crystals were obtained using 0.1 Msodium citrate pH 5.6, 0.1 MNaCl, 15% PEG 400 as precipitant. The crystals diffracted to 2.25 Å resolution using synchrotron radiation and belonged to the monoclinic space groupC2, with unit-cell parametersa= 156.521,b= 88.991,c= 158.971 Å, β = 107.144°. Data were collected at the BL-38B1 station of SPring-8 (Hyogo, Japan).

scholarly journals Preliminary crystallographic studies of aSchistosoma mansoniantigen (Sm21.7) dynein light-chain (DLC) domain

2014 ◽  
Vol 70 (6) ◽  
pp. 803-807 ◽  
Author(s):  
M. A. F. Costa ◽  
F. T. G. Rodrigues ◽  
B. C. A. Chagas ◽  
C. M. F. Rezende ◽  
A. M. Goes ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Monomethyl Ether ◽  
Dynein Light Chain ◽  
X Ray Diffraction ◽  
Three Dimensional Model ◽  
Major Health Problem ◽  
X Ray ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Drug Of Choice

Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) fromSchistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed inEscherichia coliand the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space groupP6122, with similar unit-cell parametersa=b= 108.5,c= 55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS–PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine.

A novel representative in the rare family of trivanadates, KMn2V3O10: synthesis, crystal structure and magnetic properties

2018 ◽  
Vol 74 (1) ◽  
pp. 97-103 ◽  
Author(s):  
Olga Yakubovich ◽  
Larisa Shvanskaya ◽  
Zlata Pchelkina ◽  
Olga Dimitrova ◽  
Anatoliy Volkov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Exchange Interactions ◽  
Potassium Ions ◽  
The Novel ◽  
First Principles Calculations ◽  
X Ray Diffraction ◽  
Magnetic Exchange ◽  
Cell Parameters ◽  
Magnetic Couplings

Potassium dimanganese trivanadate, KMn2V3O10, was synthesized hydrothermally and its crystal structure was determined from single-crystal X-ray diffraction data. The novel phase crystallizes with triclinic symmetry in space group P\bar 1 with unit-cell parameters of a = 6.912 (5), b = 6.993 (5), c = 9.656 (5) Å, α = 101.858 (5), β = 102.627 (5), γ = 100.669 (5)°, Z = 2 and V = 432.6 (5) Å3. Its structure is built from tetramers of MnO6 octahedra sharing edges and trimers of VO4 tetrahedra sharing vertices. These main structural fragments are linked in a three-dimensional framework with channels occupied by potassium ions. The transformation of this structure to that of interconnected NaCa3Mn(V3O10)(V2O7) is discussed. The title compound orders antiferromagnetically at T N = 8.2 K due to the magnetic exchange interactions between tetramers of Mn octahedra through VO4 tetrahedra. First-principles calculations show the magnetic couplings via Mn—O—Mn and Mn—O—V—O—Mn pathways.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals Preliminary crystallographic analysis of Xyn52B2, a GH52 β-D-xylosidase fromGeobacillus stearothermophilusT6

2014 ◽  
Vol 70 (12) ◽  
pp. 1675-1682 ◽  
Author(s):  
Roie Dann ◽  
Shifra Lansky ◽  
Noa Lavid ◽  
Arie Zehavi ◽  
Valery Belakhov ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Crystal Form ◽  
Thermophilic Bacterium ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Cell Parameters ◽  
Average Unit

Geobacillus stearothermophilusT6 is a thermophilic bacterium that possesses an extensive hemicellulolytic system, including over 40 specific genes that are dedicated to this purpose. For the utilization of xylan, the bacterium uses an extracellular xylanase which degrades xylan to decorated xylo-oligomers that are imported into the cell. These oligomers are hydrolyzed by side-chain-cleaving enzymes such as arabinofuranosidases, acetylesterases and a glucuronidase, and finally by an intracellular xylanase and a number of β-xylosidases. One of these β-xylosidases is Xyn52B2, a GH52 enzyme that has already proved to be useful for various glycosynthesis applications. In addition to its demonstrated glycosynthase properties, interest in the structural aspects of Xyn52B2 stems from its special glycoside hydrolase family, GH52, the structures and mechanisms of which are only starting to be resolved. Here, the cloning, overexpression, purification and crystallization of Xyn52B2 are reported. The most suitable crystal form that has been obtained belonged to the orthorhombicP212121space group, with average unit-cell parametersa = 97.7,b= 119.1,c = 242.3 Å. Several X-ray diffraction data sets have been collected from flash-cooled crystals of this form, including the wild-type enzyme (3.70 Å resolution), the E335G catalytic mutant (2.95 Å resolution), a potential mercury derivative (2.15 Å resolution) and a selenomethionine derivative (3.90 Å resolution). These data are currently being used for detailed three-dimensional structure determination of the Xyn52B2 protein.

scholarly journals Lead-antimony sulfosalts from Tuscany (Italy). XVIII. New data on the crystal-chemistry of boscardinite

2017 ◽  
Vol 81 (1) ◽  
pp. 47-60 ◽  
Author(s):  
Cristian Biagioni ◽  
Yves Moëlo
Keyword(s):  
Single Crystal ◽  
Diffraction Study ◽  
Type Specimen ◽  
Structural Features ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Mineral Associations ◽  
Crystal Chemical Data ◽  
New Findings

AbstractBoscardinite, ideally TlPb4(Sb7As2)∑9S18, has been described recently as a new homeotypic derivative of baumhauerite, found at Monte Arsiccio mine, Apuan Alps, Tuscany, Italy. New findings of boscardinite in different mineral associations of this deposit have allowed the collection of new crystal-chemical data. Electron-microprobe analysis of the crystal used for the single-crystal X-ray diffraction study gave (in wt.%): Ag 1.81(5), Tl 12.60(21), Pb 17.99(12), Hg 0.14(5), As 9.36(12), Sb 33.60(27), S 23.41(30),Cl 0.06(1), total 98.97(100). On the basis of ∑Me= 14 apfu, it corresponds to Ag0.42Tl1.52Pb2.14Hg0.02(Sb6.82As3.08)∑9.90S18.04Cl0.04. With respect to the type specimen, these new findings are characterized by a strong Pb depletion, coupled with higher Tl contents, and a significant As enrichment. The single-crystal X-ray diffraction study of this (Tl,As)-enriched boscardinite confirms the structural features described for the type sample. The unit-cell parameters area= 8.1017(4),b= 8.6597(4),c= 22.5574(10) Å, α = 90.666(2), β = 97.242(2), γ = 90.850(2)°,V= 1569.63(12) Å3, space groupP̄1. The crystal structure was refined down toR1= 0.0285 on the basis of 6582 reflections withFo> 4σ(Fo). Arsenic is dominant in threeMeS3sites, compared to one in type boscardinite. The main As-enrichment is observed in the sartorite-type sub-layer. Owing to this chemical peculiarity, (Tl, As)-rich boscardinite shows alternation, alongb, of Sb-rich sites and As-rich sites; this feature represents the main factor controlling the 8 Å superstructure. The chemical variability of boscardinite is discussed; the Ag increase observed here gets closer to stoichiometric AgTl3Pb4(Sb14As6)∑20S36(Z= 1), against possible extension up to AgTl2Pb6(Sb15As4)∑19S36for type boscardinite.

scholarly journals PicW2 fromPicea wilsonii: preparation, purification, crystallization and X-ray diffraction analysis

2018 ◽  
Vol 74 (6) ◽  
pp. 363-366 ◽  
Author(s):  
Bei Zhang ◽  
Gangxing Guo ◽  
Fang Lu ◽  
Ying Song ◽  
Yong Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Gel Filtration ◽  
Three Dimensional ◽  
Temperature Tolerance ◽  
Diffusion Method ◽  
Limiting Factor ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Low temperature is a major limiting factor for plant growth and development. Dehydrin proteins are generally induced in response to low-temperature stress. In previous research, a full-length dehydrin gene,PicW2, was isolated fromPicea wilsoniiand its expression was associated with hardiness to cold. In order to gain insight into the mechanism of low-temperature tolerance by studying its three-dimensional crystal structure, prokaryotically expressed PicW2 dehydrin protein was purified using chitosan-affinity chromatography and gel filtration, and crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 MHEPES pH 8.0, 25%(w/v) PEG 3350 using 4 mg ml−1protein solution at 289 K. X-ray diffraction data were collected from a crystal at 100 K to 2.82 Å resolution. The crystal belonged to space groupC121, with unit-cell parametersa= 121.55,b= 33.26,c= 73.39 Å, α = γ = 90.00, β = 109.01°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.87 Å3 Da−1and a solvent content of 57.20%. Owing to a lack of structures of homologous dehydrin proteins, molecular-replacement trials failed. Data collection for selenium derivatization of PicW2 and crystal structure determination is currently in progress.

scholarly journals Synthesis, Structural Features, and Catalytic Activity of an Iron(II) 3D Coordination Polymer Driven by an Ether-Bridged Pyridine-Dicarboxylate

Crystals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 369 ◽  
Author(s):  
Na Zhao ◽  
Yu Li ◽  
Jinzhong Gu ◽  
Marina V. Kirillova ◽  
Alexander M. Kirillov
Keyword(s):  
Coordination Polymer ◽  
Three Dimensional ◽  
Topological Type ◽  
Structural Features ◽  
Organic N ◽  
Catalyst Precursor ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
Oxidative Functionalization ◽  
Diffraction Structure

New iron(II) three-dimensional coordination polymer (3D CP), [Fe(µ3-Hcpna)2]n (1), was assembled under hydrothermal conditions from 5-(4’-carboxyphenoxy)nicotinic acid (H2cpna) as a trifunctional organic N,O-building block. This stable microcrystalline CP was characterized by standard methods for coordination compounds in the solid state (infrared spectroscopy, elemental analysis, thermogravimetric analysis, powder and single-crystal X-ray diffraction). Structure and topology of 1 were examined and permitted an identification of a 3,6-connected framework of the rtl topological type. In addition, compound 1 acts as effective catalyst precursor for oxidative functionalization of alkanes (propane and cyclic C5−C8 alkanes) under homogeneous catalysis conditions, namely for the oxidation of saturated hydrocarbons with H2O2/H+ system to produce ketones and alcohols, and for alkane carboxylation with CO/H2O/S2O82− system to obtain carboxylic acids. The influence of an acid promoter and substrate scope (propane and cyclic C5−C8 alkanes) were investigated.

The new P-chalcopyrite compound Cu2FeIn2Se5; synthesis, thermal analysis (DTA), and crystal structure analysis by X-ray powder diffraction (XRPD)

2021 ◽  
Vol 67 (1 Jan-Feb) ◽  
pp. 18
Author(s):  
G. E. Delgado ◽  
P. Grima-Gallardo ◽  
J. A. Aitken ◽  
A. Cárdenas ◽  
I. Brito
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Chalcopyrite Structure ◽  
Distribution Analysis ◽  
X Ray Diffraction ◽  
Quaternary Compound ◽  
X Ray ◽  
Cell Parameters

The Cu2FeIn2Se5 alloy, belonging to the system (CuInSe2)1-x(FeSe)x with x= ⅓, was synthesized by the melt and annealing technique. The differential thermal analysis (DTA) indicates that this compound melts at 1017 K. The crystal structure of this new quaternary compound was established using powder X-ray diffraction. Cation distribution analysis indicates that this material crystallizes in a P-chalcopyrite structure, space group P2c (Nº 112), with unit cell parameters a = 6.1852(2) Å, c = 12.3633(9) Å, V = 472.98(4) Å3. Cu2FeIn2Se5 is a new adamantane type compound derivative of the sphalerite structure, and consists of a three-dimensional arrangement of distorted CuSe4, FeSe4, and InSe4 tetrahedral connected by common faces.

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