scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals Purification, crystallization and preliminary X-ray data collection of the N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 fromMus musculus

2014 ◽  
Vol 70 (5) ◽  
pp. 611-615
Author(s):  
Wentao Diao ◽  
Xue Yang ◽  
Hao Zhou
Keyword(s):  
Unit Cell ◽  
26S Proteasome ◽  
Regulatory Subunit ◽  
Atpase Domain ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

The protein 26S proteasome regulatory subunit p27 is one of the four chaperones that help in the assembly of the 19S regulatory particle (RP) of the 26S proteasome. In the present work, the N-terminus of p27 (residues 1–128) fromMus musculuswas cloned, expressed, purified and crystallized alone and in complex with the C-terminal ATPase domain of Rpt5 (residues 173–442). The crystals of p27(1–128)diffracted to 1.7 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 26.79,b= 30.39,c= 145.06 Å. Resolution-dependent Matthews coefficient probability analysis suggested the presence of only one molecule per asymmetric unit, with 40.5% solvent content and aVMvalue of 2.02 Å3 Da−1. The crystal of the p27(1–128)–Rpt5(173–442)complex diffracted to 4 Å resolution and belonged to space groupP222, with unit-cell parametersa= 75.93,b= 76.08,c= 336.85 Å. The presence of four heterodimers in the asymmetric unit with 53.2% solvent content and aVMvalue of 2.63 Å3 Da−1or five heterodimers in the asymmetric unit with 41.5% solvent content and aVMvalue of 2.10 Å3 Da−1is assumed.

Crystallization and preliminary X-ray diffraction analysis of hydroxynitrile lyase from cassava (Manihot esculenta)

1999 ◽  
Vol 55 (4) ◽  
pp. 904-906 ◽  
Author(s):  
Hanspeter Lauble ◽  
Klaas Decanniere ◽  
Harald Wajant ◽  
Siegfried Förster ◽  
Franz Effenberger
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
Hydroxynitrile Lyase ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Hydroxynitrile lyase from M. esculenta (cassava) was crystallized in two different crystal forms by the hanging-drop vapour-diffusion method. Crystals of form I were obtained from a mixture of polyethylene glycol 8000 and 2-methyl-2,4-pentanediol, and belong to the tetragonal space group P41212 or its enantiomorph P43212, with unit-cell parameters a  =  b  =  105.9, c  =  188.9 Å and with two molecules in the asymmetric unit. These crystals diffract to 2.9 Å with conventional X-ray sources and beyond 2.1 Å resolution with synchrotron radiation. The crystals are relatively sensitive to radiation damage and conditions for flash-cooling the crystals have been established. A complete native data set has been collected up to 2.2 Å resolution. Crystal form II has been obtained at pH 5.6 using lithium sulfate as a precipitant. The crystals apparently belong to the orthorhombic space group P21212, with unit-cell parameters a = 117.52, b = 127.09 and c = 78.08 Å, have two molecules in the asymmetric unit and diffract to beyond 2.0 Å resolution. A complete native data set has been collected to 2.2 Å resolution.

scholarly journals Crystallization and X-ray diffraction analysis of anL-arabinonate dehydratase fromRhizobium leguminosarumbv.trifoliiand aD-xylonate dehydratase fromCaulobacter crescentus

2016 ◽  
Vol 72 (8) ◽  
pp. 604-608 ◽  
Author(s):  
Mohammad Mubinur Rahman ◽  
Martina Andberg ◽  
Anu Koivula ◽  
Juha Rouvinen ◽  
Nina Hakulinen
Keyword(s):  
Rhizobium Leguminosarum ◽  
Caulobacter Crescentus ◽  
Sodium Formate ◽  
Unit Cell ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
Cell Parameters

L-Arabinonate dehydratase (EC 4.2.1.25) and D-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. L-Arabinonate dehydratase converts L-arabinonate into 2-dehydro-3-deoxy-L-arabinonate, and D-xylonate dehydratase catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-xylonate. L-Arabinonate and D-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any L-arabinonate or D-xylonate dehydratase is available in the PDB. In this study, recombinant L-arabinonate dehydratase fromRhizobium leguminosarumbv.trifolii(RlArDHT) and D-xylonate dehydratase fromCaulobacter crescentus(CcXyDHT) were heterologously expressed inEscherichia coliand purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals ofRlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space groupP21, with unit-cell parametersa = 106.07,b= 208.61,c= 147.09 Å, β = 90.43°. EightRlArDHT molecules (two tetramers) in the asymmetric unit give aVMvalue of 3.2 Å3 Da−1and a solvent content of 62%. Crystals ofCcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space groupC2, with unit-cell parametersa= 270.42,b= 236.13,c = 65.17 Å, β = 97.38°. FourCcXyDHT molecules (a tetramer) in the asymmetric unit give aVMvalue of 4.0 Å3 Da−1and a solvent content of 69%.

Crystallization and preliminary X-ray studies of sialidase L from the leech Macrobdella decora

1998 ◽  
Vol 54 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Yu Luo ◽  
Min-yuan Chou ◽  
Su-chen Li ◽  
Yu-teh Li ◽  
Ming Luo
Keyword(s):  
Escherichia Coli ◽  
Unit Cell ◽  
Data Sets ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Mercury Derivative ◽  
Macrobdella Decora

Functional monomeric 83 kDa sialidase L, a NeuAcα2→3Gal-specific sialidase from Macrobdella leech, was expressed in Escherichia coli and readily crystallized by a macroseeding technique. The crystal belongs to space group P1 with unit-cell parameters a = 46.4, b = 69.3, c = 72.5 Å, α = 113.5, β = 95.4 and γ = 107.3°. There is one molecule per unit cell, giving a Vm = 2.4 Å3 Da−1 and a solvent content of 40%. Native and mercury-derivative data sets were collected to 2.0 Å resolution. Threading and molecular-replacement calculations confirmed the existence of a bacterial sialidase-like domain.

The solid solution TbNiIn1−x Ga x

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Myroslava Horiacha ◽  
Galyna Nychyporuk ◽  
Rainer Pöttgen ◽  
Vasyl Zaremba
Keyword(s):  
Solid Solution ◽  
Unit Cell ◽  
Type Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Structure Space ◽  
Arc Melting

Abstract Phase formation in the solid solution TbNiIn1−x Ga x at 873 K was investigated in the full concentration range by means of powder X-ray diffraction and EDX analysis. The samples were synthesized by arc-melting of the pure metals with subsequent annealing at 873 K for one month. The influence of the substitution of indium by gallium on the type of structure and solubility was studied. The solubility ranges have been determined and changes of the unit cell parameters were calculated on the basis of powder X-ray diffraction data: TbNiIn1–0.4Ga0–0.6 (ZrNiAl-type structure, space group P 6 ‾ 2 m $P‾{6}2m$ , a = 0.74461(8)–0.72711(17) and c = 0.37976(5)–0.37469(8) nm); TbNiIn0.2–0Ga0.8–1.0 (TiNiSi-type structure, space group Pnma, а = 0.68950(11)–0.68830(12), b = 0.43053(9)–0.42974(6), с = 0.74186(10)–0.73486(13) nm). The crystal structures of TbNiGa (TiNiSi type, Pnma, a = 0.69140(5), b = 0.43047(7), c = 0.73553(8) nm, wR2=0.0414, 525 F 2 values, 21 variables), TbNiIn0.83(1)Ga0.17(1) (ZrNiAl type, P 6 ‾ 2 m $P‾{6}2m$ , a = 0.74043(6), c = 0.37789(3) nm, wR2 = 0.0293, 322 F 2 values, 16 variables) and TbNiIn0.12(2)Ga0.88(2) (TiNiSi type, Pnma, a = 0.69124(6), b = 0.43134(9), c = 0.74232(11) nm, wR2 = 0.0495, 516 F 2 values, 21 variables) have been determined. The characteristics of the solid solutions and the variations of the unit cell parameters are briefly discussed.

scholarly journals Crystal Chemistry and High-Temperature Behaviour of Ammonium Phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O from the Burned Dumps of the Chelyabinsk Coal Basin

Minerals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 486 ◽  
Author(s):  
Andrey A. Zolotarev ◽  
Elena S. Zhitova ◽  
Maria G. Krzhizhanovskaya ◽  
Mikhail A. Rassomakhin ◽  
Vladimir V. Shilovskikh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Temperature ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Coal Basin ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Mineral Phases

The technogenic mineral phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O from the burned dumps of the Chelyabinsk coal basin have been investigated by single-crystal X-ray diffraction, scanning electron microscopy and high-temperature powder X-ray diffraction. The NH4MgCl3·6H2O phase is monoclinic, space group C2/c, unit cell parameters a = 9.3091(9), b = 9.5353(7), c = 13.2941(12) Å, β = 90.089(8)° and V = 1180.05(18) Å3. The crystal structure of NH4MgCl3·6H2O was refined to R1 = 0.078 (wR2 = 0.185) on the basis of 1678 unique reflections. The (NH4)2Fe3+Cl5·H2O phase is orthorhombic, space group Pnma, unit cell parameters a = 13.725(2), b = 9.9365(16), c = 7.0370(11) Å and V = 959.7(3) Å3. The crystal structure of (NH4)2Fe3+Cl5·H2O was refined to R1 = 0.023 (wR2 = 0.066) on the basis of 2256 unique reflections. NH4MgCl3·6H2O is stable up to 90 °C and then transforms to the less hydrated phase isotypic to β-Rb(MnCl3)(H2O)2 (i.e., NH4MgCl3·2H2O), the latter phase being stable up to 150 °C. (NH4)2Fe3+Cl5·H2O is stable up to 120 °C and then transforms to an X-ray amorphous phase. Hydrogen bonds provide an important linkage between the main structural units and play the key role in determining structural stability and physical properties of the studied phases. The mineral phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O are isostructural with natural minerals novograblenovite and kremersite, respectively.

scholarly journals Bulachite, [Al6(AsO4)3(OH)9(H2O)4]⋅2H2O from Cap Garonne, France: Crystal structure and formation from a higher hydrate

2020 ◽  
Vol 84 (4) ◽  
pp. 608-615
Author(s):  
Ian E. Grey ◽  
Emre Yoruk ◽  
Stéphanie Kodjikian ◽  
Holger Klein ◽  
Catherine Bougerol ◽  
...  
Keyword(s):  
Unit Cell ◽  
Orthorhombic Symmetry ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Different Temperatures ◽  
Using Data ◽  
Hydrated Aluminium

AbstractBulachite specimens from Cap Garonne, France, comprise two intimately mixed hydrated aluminium arsenate minerals with the same Al:As ratio of 2:1 and with different water contents. The crystal structures of both minerals have been solved using data from low-dose electron diffraction tomography combined with synchrotron powder X-ray diffraction. One of the minerals has the same powder X-ray diffraction pattern (PXRD) as for published bulachite. It has orthorhombic symmetry, space group Pnma with unit-cell parameters a = 15.3994(3), b = 17.6598(3), c = 7.8083(1) Å and Z = 4, with the formula [Al6(AsO4)3(OH)9(H2O)4]⋅2H2O. The second mineral is a higher hydrate with composition [Al6(AsO4)3(OH)9(H2O)4]⋅8H2O. It has the same Pnma space group and unit-cell parameters a = 19.855(4), b = 17.6933(11) and c = 7.7799(5) Å i.e. almost the same b and c parameters but a much larger a parameter. The structures are based on polyhedral layers, parallel to (100), of composition [Al6(AsO4)3(OH)9(H2O)4] and with H-bonded H2O between the layers. The layers contain [001] spiral chains of edge-shared octahedra, decorated with corner connected AsO4 tetrahedra that are the same as in the mineral liskeardite. The spiral chains are joined together by octahedral edge-sharing to form layers parallel to (100). Synchrotron PXRD patterns collected at different temperatures during heating of the specimen show that the higher-hydrate mineral starts transforming to bulachite when heated to 50°C, and the transformation is complete between 75 and 100°C.

scholarly journals Cloning, purification, crystallization and preliminary X-ray diffraction of the OleC protein fromStenotrophomonas maltophiliainvolved in head-to-head hydrocarbon biosynthesis

2010 ◽  
Vol 66 (9) ◽  
pp. 1108-1110 ◽  
Author(s):  
Janice A. Frias ◽  
Brandon R. Goblirsch ◽  
Lawrence P. Wackett ◽  
Carrie M. Wilmot
Keyword(s):  
Diffraction Data ◽  
Unit Cell ◽  
Biosynthetic Enzyme ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Hydrocarbon Biosynthesis

OleC, a biosynthetic enzyme involved in microbial hydrocarbon biosynthesis, has been crystallized. Synchrotron X-ray diffraction data have been collected to 3.4 Å resolution. The crystals belonged to space groupP3121 orP3221, with unit-cell parametersa=b= 98.8,c= 141.0 Å.

X-ray diffraction data of Ti2O2(C2O4)(OH)2·H2O

1994 ◽  
Vol 9 (3) ◽  
pp. 187-188 ◽  
Author(s):  
Hee-Lack Choi ◽  
Naoya Enomoto ◽  
Nobuo Ishizawa ◽  
Zenbe-e Nakagawa
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal System

X-ray powder diffraction data for Ti2O2(C2O4)(OH)2·H2O were obtained. The crystal system was determined to be orthorhombic with space group C2221. The unit cell parameters were refined to a = 1.0503(2) nm, b = 1.5509(3) nm, and c = 0.9700(1) nm.

scholarly journals Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c fromMycobacterium tuberculosis

2014 ◽  
Vol 70 (8) ◽  
pp. 1090-1092
Author(s):  
Feifei Lu ◽  
Feng Gao ◽  
Honglin Li ◽  
Weimin Gong ◽  
Lin Zhou ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Unit Cell ◽  
Diffusion Method ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion

The conserved protein Rv3705c fromMycobacterium tuberculosishas been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space groupP6122 orP6522, with unit-cell parametersa=b= 198.0,c= 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å.

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