scholarly journals Sequence Analysis and Preliminary X-ray Crystallographic Analysis of an Acetylesterase (LgEstI) from Lactococcus garvieae

Crystals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 46
Author(s):  
Hackwon Do ◽  
Ying Wang ◽  
Chang Woo Lee ◽  
Wanki Yoo ◽  
Sangeun Jeon ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Engineering ◽  
Model Building ◽  
Structure Refinement ◽  
Crystallographic Analysis ◽  
Wild Type ◽  
Acetyl Esterase ◽  
X Ray ◽  
Lactococcus Garvieae ◽  
Replacement Method

A gene encoding LgEstI was cloned from a bacterial fish pathogen, Lactococcus garvieae. Sequence and bioinformatic analysis revealed that LgEstI is close to the acetyl esterase family and had maximum similarity to a hydrolase (UniProt: Q5UQ83) from Acanthamoeba polyphaga mimivirus (APMV). Here, we present the results of LgEstI overexpression and purification, and its preliminary X-ray crystallographic analysis. The wild-type LgEstI protein was overexpressed in Escherichia coli, and its enzymatic activity was tested using p-nitrophenyl of varying lengths. LgEstI protein exhibited higher esterase activity toward p-nitrophenyl acetate. To better understand the mechanism underlying LgEstI activity and subject it to protein engineering, we determined the high-resolution crystal structure of LgEstI. First, the wild-type LgEstI protein was crystallized in 0.1 M Tris-HCl buffer (pH 7.1), 0.2 M calcium acetate hydrate, and 19% (w/v) PEG 3000, and the native X-ray diffraction dataset was collected up to 2.0 Å resolution. The crystal structure was successfully determined using a molecular replacement method, and structure refinement and model building are underway. The upcoming complete structural information of LgEstI may elucidate the substrate-binding mechanism and provide novel strategies for subjecting LgEstI to protein engineering.

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.

The Meisenheimer rearrangement in heterocyclic synthesis. II. Synthesis and X-ray crystal structure of a tetrahydro-1H-2,3-benzoxazocine and preparation of a hexahydro-2,3-benzoxazonine

1980 ◽  
Vol 33 (6) ◽  
pp. 1323 ◽  
Author(s):  
JB Bremner ◽  
EJ Browne ◽  
PE Davies ◽  
CLWAH Raston
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Acetic Acid ◽  
Crystal And Molecular Structure ◽  
Phosphorus Oxychloride ◽  
Crystallographic Analysis ◽  
Heterocyclic Synthesis ◽  
Reaction Conditions ◽  
X Ray ◽  
Heterocyclic Derivatives

The heterocyclic derivatives, 8,9-dimethoxy-3-methyl-1-phenyl-3,4,5,6- tetrahydro-1H-2,3-benzoxazocine(3a) and 9,10-dimethoxy-3-methyl-1- phenyl-1,3,4,5,6,7-hexahydro-2,3-benzoxazonine (3b),examples of two new ring systems, have been prepared by Meisenheimer rearrangement of the corresponding 2-benzazepine and 2-benzazocine N-oxide derivatives (2a) and (2b). The Bischler-Napieralski-type cyclization reaction was used in the preparation of the tertiary amine precursors of these N-oxides reaction conditions for the cyclization were critical and phosphorus oxychloride in refluxing butanenitrile was found to give the best yields of the seven- or eight-membered cyclic imine intermediates. Reductive cleavage of the benzoxazocine derivative (3a) with zinc in acetic acid followed by N-methylation gave the expected product, [2-{3- (dimethylamino)propyl}-4,5-di-methoxyphenyl]phenylmethanol (12). The crystal and molecular structure of (3a) has been determined by X-ray crystallographic analysis.

A Novel Alkali-Metal Hydrido-tris(pyrazolyl)borate (Tp*) Complex. Isolation and Crystal Structure of [(Me2CO)3(NaTp*)2]

2014 ◽  
Vol 69 (7) ◽  
pp. 793-798
Author(s):  
Laurent Plasseraud ◽  
Hélène Cattey
Keyword(s):  
Crystal Structure ◽  
Alkali Metal ◽  
Sodium Hydroxide ◽  
Title Compound ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Large Excess ◽  
X Ray ◽  
Acetone Water

The title compound was isolated from the treatment of Tp*Sn(Cl)2Bu (1) with a large excess of sodium hydroxide in a mixture of acetone-water at room temperature. [(Me2CO)3(NaTp*)2] (2) crystallizes at 4 °C as prismatic colorless crystals, in the monoclinic space group P21/c with Z = 4, a = 12.2837(6), b = 24.3197(12), c = 16.9547(8) Å, β = 110.017(1)°, and V = 4759.0(4) Å3. The X-ray crystallographic analysis revealed a dinuclear unit in which two Tp*Na moieties are held together by three bridging acetone molecules acting as oxygen-based donors.

Crystal structure of potassium tetraperoxomolybdate (VI) K2[Mo(O2)4]

2005 ◽  
Vol 20 (3) ◽  
pp. 203-206 ◽  
Author(s):  
M. Grzywa ◽  
M. Różycka ◽  
W. Łasocha
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Diffraction Pattern ◽  
Powder Diffraction ◽  
Rietveld Method ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters

Potassium tetraperoxomolybdate (VI) K2[Mo(O2)4] was prepared, and its X-ray powder diffraction pattern was recorded at low temperature (258 K). The unit cell parameters were refined to a=10.7891(2) Å, α=64.925(3)°, space group R−3c (167), Z=6. The compound is isostructural with potassium tetraperoxotungstate (VI) K2[W(O2)4] (Stomberg, 1988). The sample of K2[Mo(O2)4] was characterized by analytical investigations, and the results of crystal structure refinement by Rietveld method are presented; final RP and RWP are 9.79% and 12.37%, respectively.

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.

scholarly journals Recommended X-ray single-crystal structure refinement and Rietveld refinement procedure for tremolite

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Paolo Ballirano ◽  
Beatrice Celata ◽  
Alessandro Pacella ◽  
Ferdinando Bosi
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Rietveld Refinement ◽  
Structure Refinement ◽  
Point Of View ◽  
Single Crystal Structure ◽  
Crystal Structure Refinement ◽  
Statistical Point ◽  
X Ray ◽  
Refinement Procedure

A detailed description of the structure of the amphibole-supergroup minerals is very challenging owing to their complex chemical composition that renders the process of cation partition extremely difficult, particularly because of the occurrence of multivalent elements. Since amphiboles naturally occur under a fibrous morphology and have largely been used to produce asbestos, there is a growing demand for detailed and accurate structural data in order to study the relationships between structure, composition and toxicity. The present study proposes a recommended refinement procedure for both X-ray single-crystal structure refinement (SREF) and Rietveld analysis for tremolite, selected as a test case. The corresponding structural results are compared to estimate the `degree of confidence' of the Rietveld refinement with regard to SREF. In particular, it is shown that the interpretation of the electron density of the tremolite structure by SREF is model dependent. By assuming that the site-scattering values from SREF should be as close as possible to those from electron microprobe analysis, as a crucial constraint for the correct description of the final crystal-chemical model, it is found that it is best satisfied by using partially ionized scattering curves (SCs) for O and Si, and neutral SCs (neutral oxygen curves or NOCs) for other atoms. This combination leads to the best fit to the diffraction data. Moreover, it is found that Rietveld refinement using NOCs produces the best structural results, in excellent agreement with SREF. It is worth noting that, due to the complexity of the diffraction pattern and the fairly large number of freely refinable parameters, refinements with different combinations of SCs produce results almost indistinguishable from a statistical point of view, albeit showing significant differences from a structural point of view.

scholarly journals Crystal structure refinement of magnesium zinc divanadate, MgZnV2O7, from powder X-ray diffraction data

2021 ◽  
Vol 77 (6) ◽  
pp. 588-591
Author(s):  
Stephanie J. Hong ◽  
Jun Li ◽  
Mas A. Subramanian
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Atomic Ratio ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Trigonal Bipyramidal ◽  
Wyckoff Position ◽  
Distorted Trigonal Bipyramidal

The crystal structure of magnesium zinc divanadate, MgZnV2O7, was determined and refined from laboratory X-ray powder diffraction data. The title compound was synthesized by a solid-state reaction at 1023 K in air. The crystal structure is isotypic with Mn0.6Zn1.4V2O7 (C2/m; Z = 6) and is related to the crystal structure of thortveitite. The asymmetric unit contains two metal sites with statistically distributed magnesium and zinc atoms with the atomic ratio close to 1:1. One (Mg/Zn) metal site (M1) is located on Wyckoff position 8j and the other (M2) on 4h. Three V sites (all on 4i), and eight O (three 8j, four 4i, and one 2b) sites complete the asymmetric unit. The structure is an alternate stacking of V2O7 layers and (Mg/Zn) atom layers along [20\overline{1}]. It is distinct from other related structures in that each V2O7 layer consists of two groups: a V2O7 dimer and a V4O14 tetramer. Mixed-occupied M1 and M2 are coordinated by oxygen atoms in distorted trigonal bipyramidal and octahedral sites, respectively.

Microporous crystal structure of labuntsovite-Fe and high-pressure behavior up to 23 GPa

2018 ◽  
Vol 74 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Sergey M. Aksenov ◽  
Elena A. Bykova ◽  
Ramiza K. Rastsvetaeva ◽  
Nikita V. Chukanov ◽  
Irina P. Makarova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Single Crystal ◽  
Cross Section ◽  
Structure Refinement ◽  
Alkaline Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Diamond Anvil ◽  
The Stability

Labuntsovite-Fe, an Fe-dominant member of the labuntsovite subgroup, was first discovered in the Khibiny alkaline massif on Mt Kukisvumchorr [Khomyakov et al. (2001). Zap. Vseross. Mineral. Oba, 130, 36–45]. However, no data are published about the crystal structure of this mineral. Labuntsovite-Fe from a peralkaline pegmatite located on Mt Nyorkpakhk, in the Khibiny alkaline complex, Kola Peninsula, Russia, has been investigated by means of electron microprobe analyses, single-crystal X-ray structure refinement, and IR and Raman spectroscopies. Monoclinic unit-cell parameters of labuntsovite-Fe are: a = 14.2584 (4), b = 13.7541 (6), c = 7.7770 (2) Å, β = 116.893 (3)°; V = 1360.22 (9) Å3; space group C2/m. The structure was refined to final R 1 = 0.0467, wR 2 = 0.0715 for 3202 reflections [I > 3σ(I)]. The refined crystal chemical formula is (Z = 2): Na2K2Ba0.7[(Fe0.5Ti0.1Mg0.05)(H2O)1.3]{[Ti2(Ti1.9Nb0.1)(O,OH)4][Si4O12]2}·4H2O. The high-pressure in situ single-crystal X-ray diffraction study of the labuntsovite-Fe has been carried out in a diamond anvil cell. The labuntsovite-type structure is stable up to 23 GPa and phase transitions are not observed. Calculations using the BM3 equation of state resulted in the bulk modulus K = 72 (2) GPa, K′0 = 3.7 (2) and V 0 = 1363 (2) Å3. Compressing of the heteropolyhedral zeolite-like framework leads to the deformation of main structural units. Octahedral rods show the gradual increase of distortion and the wave-like character of rods becomes more distinct. Rod deformations result in the distortion of the silicon–oxygen ring which is not equal in different directions. Structural channels are characterized by a different ellipticity–pressure relationship: the cross-section of the largest channel I and channel II demonstrates the stability of the geometrical characteristics which practically do not depend on pressure: ∊channel I ≃ 0.85 (4) (cross-section is rather regular) and ∊channel II ≃ 0.52 (2) within the whole pressure range. However, channel III is characterized by the increasing of ellipticity with pressure (∊ = 0.40 → 0.10).

Synthesen, Kristallstrukturen und magnetische Eigenschaften von [Li(12-Krone-4)2][Li(12-Krone-4)(OH2)]2[Nb6Cl18], [Li(15-Krone-5)2(OH2)]3[Nb6Cl18] und [(18-Krone-6)2(O2H5)]3[Nb6Cl18] / Syntheses, Crystal Structures and Magnetic Behaviour of [Li(12-Krone-4)2][Li(12-Krone-4)(OH2)]2[Nb6Cl18], [Li(15-Krone-5)2(OH2)]3[Nb6Cl18] and [(18-Krone-6)2(O2H5)]3[Nb6Cl18]

2001 ◽  
Vol 56 (10) ◽  
pp. 1025-1034 ◽  
Author(s):  
Markus Ströbele ◽  
H.-Jtirgen Meyer
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Crown Ethers ◽  
Magnetic Measurements ◽  
Structure Refinement ◽  
Magnetic Behaviour ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Paramagnetic Behaviour

The title compounds were prepared through reactions of Li2Nb6Cl16 with the corresponding crown ethers in acetone. All three compounds were obtained as dark brown crystals. Their structures were solved with the means of single-crystal X-ray diffraction.[Li(12-crown-4)2][Li(12-crown-4)(OH2)]2[Nb6Cl18]: space group P21/n, Z =2, a = 1320.4(1), b = 1879.1(1), c = 1321.7(1) pm, ß = 92.515(6)°, R1 = 0.0297 (I>2σ(I)). The crystal structure contains Li+ sandwiched by two 12-crown-4-ethers plus Li+ coordinated by one 12-crown-4- ether and one water molecule.[Li(15-crown-5)2(OH2)]3[Nb6Cl18]: space group R3̅, Z = 3, a = b = 2081.7(1), c = 1991.7(1) pm, R1 = 0.0395 (I > 2σ(I)). In the crystal structure Li+ and one water molecule are sandwiched by two 15-crown-5-ethers.[(18-crown-6)2(O2H5)]3[Nb6Cl18]: space group P1̅, Z = 1 ,a = 1405.1(1), b = 1461.1(2), c = 1492.2(2) pm; α = 98.80(1)°, ß = 98.15(1)°, γ = 97.41(1)°, R1 = 0.0538 (I > 2σ(I)). H5O2+ was found in the structure refinement sandwiched between two 18-crown-6-ethers.All compounds reported contain [Nb6Cl18] clusters with Nb-Nb distances between 299 and 301 pm. The paramagnetic behaviour expected for [Nb6Cl18]3- in all three compounds was confirmed by magnetic measurements.

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