scholarly journals Structure of the kinase domain of Gilgamesh fromDrosophila melanogaster

2014 ◽  
Vol 70 (4) ◽  
pp. 438-443 ◽  
Author(s):  
Ni Han ◽  
CuiCui Chen ◽  
Zhubing Shi ◽  
Dianlin Cheng
Keyword(s):  
Kinase Domain ◽  
Unit Cell ◽  
Molecular Replacement ◽  
Active Conformation ◽  
Structural Comparison ◽  
Unit Cell Parameters ◽  
Hedgehog Signalling ◽  
Space Group ◽  
Cell Parameters ◽  
And Function

The CK1 family kinases regulate multiple cellular aspects and play important roles in Wnt/Wingless and Hedgehog signalling. The kinase domain ofDrosophilaGilgamesh isoform I (Gilgamesh-I), a homologue of human CK1-γ, was purified and crystallized. Crystals of methylated Gilgamesh-I kinase domain with a D210A mutation diffracted to 2.85 Å resolution and belonged to space groupP43212, with unit-cell parametersa=b= 52.025,c= 291.727 Å. The structure of Gilgamesh-I kinase domain, which was determined by molecular replacement, has conserved catalytic elements and an active conformation. Structural comparison indicates that an extended loop between the α1 helix and the β4 strand exists in the Gilgamesh-I kinase domain. This extended loop may regulate the activity and function of Gilgamesh-I.

scholarly journals Purification, crystallization and initial crystallographic analysis of the α-catenin homologue HMP-1 fromCaenorhabditis elegans

2016 ◽  
Vol 72 (3) ◽  
pp. 234-239 ◽  
Author(s):  
Hyunook Kang ◽  
Injin Bang ◽  
William I. Weis ◽  
Hee-Jung Choi
Keyword(s):  
Crystallographic Analysis ◽  
Unit Cell ◽  
Molecular Replacement ◽  
Binding Region ◽  
Unit Cell Parameters ◽  
Mechanical Tension ◽  
Space Group ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Mammalian Homologue

Adherens junctions transmit mechanical force between cells. In these junctions, β-catenin binds to cadherins and to the N-terminal domain of α-catenin, which in turn binds to actin filamentsviaits C-terminal domain. The middle (M) domain of α-catenin plays an important role in responding to mechanical tension. The nematodeCaenorhabditis eleganscontains α- and β-catenin homologues called HMP-1 and HMP-2, respectively, but HMP-1 behaves differently from its mammalian homologue. Thus, structural and biochemical studies of HMP-1 have been initiated to understand the mechanism of HMP-1 and the evolution of α-catenin. The N-terminal domain of HMP-1 in complex with the minimal HMP-1-binding region of HMP-2 was purified and crystallized. These crystals diffracted to 1.6 Å resolution and belonged to space groupP3121, with unit-cell parametersa=b= 57.1,c= 155.4 Å. The M domain of HMP-1 was also purified and crystallized. The M-domain crystals diffracted to 2.4 Å resolution and belonged to space groupP212121, with unit-cell parametersa = 72.8,b= 81.5,c = 151.4 Å. Diffraction data were collected and processed from each crystal, and the structures were solved by molecular replacement.

scholarly journals Structures of theN-acetyltransferase domain ofXylella fastidiosaN-acetyl-L-glutamate synthase/kinase with and without a His tag bound toN-acetyl-L-glutamate

2015 ◽  
Vol 71 (1) ◽  
pp. 86-95 ◽  
Author(s):  
Gengxiang Zhao ◽  
Zhongmin Jin ◽  
Norma M. Allewell ◽  
Mendel Tuchman ◽  
Dashuang Shi
Keyword(s):  
Glutamate Synthase ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Product Release ◽  
His Tag ◽  
And Function ◽  
Acetyltransferase Domain

Structures of the catalyticN-acetyltransferase (NAT) domain of the bifunctionalN-acetyl-L-glutamate synthase/kinase (NAGS/K) fromXylella fastidiosabound toN-acetyl-L-glutamate (NAG) with and without an N-terminal His tag have been solved and refined at 1.7 and 1.4 Å resolution, respectively. The NAT domain with an N-terminal His tag crystallized in space groupP41212, with unit-cell parametersa=b= 51.72,c= 242.31 Å. Two subunits form a molecular dimer in the asymmetric unit, which contains ∼41% solvent. The NAT domain without an N-terminal His tag crystallized in space groupP21, with unit-cell parametersa= 63.48,b= 122.34,c= 75.88 Å, β = 107.6°. Eight subunits, which form four molecular dimers, were identified in the asymmetric unit, which contains ∼38% solvent. The structures with and without the N-terminal His tag provide an opportunity to evaluate how the His tag affects structure and function. Furthermore, multiple subunits in different packing environments allow an assessment of the plasticity of the NAG binding site, which might be relevant to substrate binding and product release. The dimeric structure of theX. fastidiosaN-acetytransferase (xfNAT) domain is very similar to that of humanN-acetyltransferase (hNAT), reinforcing the notion that mammalian NAGS is evolutionally derived from bifunctional bacterial NAGS/K.

Crystallization and preliminary analysis of bovine adenosine deaminase

1999 ◽  
Vol 55 (12) ◽  
pp. 2031-2032 ◽  
Author(s):  
Takayoshi Kinoshita ◽  
Nobuya Nishio ◽  
Akihiro Sato ◽  
Masayoshi Murata
Keyword(s):  
Adenosine Deaminase ◽  
Ammonium Sulfate ◽  
Preliminary Analysis ◽  
Unit Cell ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Vapour Diffusion

Adenosine deaminase (ADA) from bovine intestine was crystallized with purine riboside by vapour diffusion using ammonium sulfate as precipitant. The crystals are tetragonal and have unit-cell parameters a = b = 80.03, c = 141.68 Å. They belong to space group P41212 or P43212 and diffract to at least 2.0 Å resolution. The structure is being solved by molecular replacement.

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

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.

Monoclinic and Hexagonal Nepheline Structures of (Na3/4/K1/4)AlGeO4

1998 ◽  
Vol 54 (3) ◽  
pp. 211-220 ◽  
Author(s):  
R. P. Hammond ◽  
J. Barbier
Keyword(s):  
Large Family ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Silicate Mineral ◽  
Tetrahedral Framework ◽  
Space Group ◽  
Cell Parameters ◽  
Monoclinic Form ◽  
Hexagonal Form ◽  
Alkali Atoms

Hexagonal (Na3/4K1/4)AlGeO4 crystallizes in the space group P63 with unit-cell parameters a = 10.164 (2), c = 8.540 (2) Å and Z = 8 [wR(F 2) = 0.066 for all 3060 independent reflections]. Monoclinic (Na3/4K1/4)AlGeO4 crystallizes in the space group P21 with unit-cell parameters a = 10.0477 (4), b = 8.5764 (4), c = 10.2118 (4) Å, β = 119.035 (1)° and Z = 8 [wR(F 2) = 0.120 for all 3194 independent reflections measured on a twinned crystal]. Both structures belong to the large family of stuffed tridymites, with the Al and Ge atoms occupying tetrahedral sites, and the alkali atoms occupying the cavities of the tetrahedral framework. Hexagonal (Na3/4K1/4)AlGeO4 is isostructural with the silicate mineral nepheline (Na3/4K1/4)AlSiO4, while monoclinic (Na3/4K1/4)AlGeO4 corresponds to a minor distortion of the nepheline structure. Chemical analysis by electron microprobe and structure determination of flux-grown single crystals indicate that the hexagonal form with the chemical formula (Na0.78K0.19)Al0.97Ge1.03O4 may be stabilized by an alkali deficiency similar to that found in hexagonal natural nephelines. In contrast, all alkali sites are fully occupied in the monoclinic form of composition (Na0.75K0.25)AlGeO4 and the lower symmetry eliminates the oxygen disorder present in the hexagonal form.

X-ray powder diffraction data for tetrazene nitrate monohydrate, C2H9N11O4

2021 ◽  
pp. 1-3
Author(s):  
J. Maixner ◽  
J. Ryšavý
Keyword(s):  
Cell Volume ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for tetrazene nitrate monohydrate, C2H9N11O4, are reported [a = 5.205(1) Å, b = 13.932(3) Å, c = 14.196(4) Å, β = 97.826(3)°, unit-cell volume V = 1019.8(4) Å3, Z = 4, and space group P21/c]. All measured lines were indexed and are consistent with the P21/c space group. No detectable impurities were observed.

scholarly journals Structural Transformations in Crystals Induced by Radiation and Pressure. Part 7. Molecular and Crystal Geometries as Factors Deciding about Photochemical Reactivity under Ambient and High Pressures

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 299 ◽  
Author(s):  
Krzysztof Konieczny ◽  
Arkadiusz Ciesielski ◽  
Julia Bąkowicz ◽  
Tomasz Galica ◽  
Ilona Turowska-Tyrk
Keyword(s):  
High Pressures ◽  
Unit Cell ◽  
Geometrical Parameters ◽  
Isopropyl Group ◽  
Unit Cell Parameters ◽  
Photochemical Reactivity ◽  
Space Group ◽  
Cell Parameters ◽  
Pressure Part ◽  
Asymmetric Unit Cell

We studied the photochemical reactivity of salts of 4-(2,4,6-triisopropylbenzoyl)benzoic acid with propane-1,2-diamine (1), methanamine (2), cyclohexanamine (3), and morpholine (4), for compounds (1), (3), and (4) at 0.1 MPa and for compounds (1) and (2) at 1.3 GPa and 1.0 GPa, respectively. The changes in the values of the unit cell parameters after UV irradiation and the values of the intramolecular geometrical parameters indicated the possibility of the occurrence of the Norrish–Yang reaction in the case of all the compounds. The analysis of the intramolecular geometry and free spaces revealed which o-isopropyl group takes part in the reaction. For (1), the same o-isopropyl group should be reactive at ambient and high pressures. In the case of (2), high pressure caused the phase transition from the space group I2/a with one molecule in the asymmetric unit cell to the space group P1¯ with two asymmetric molecules. The analysis of voids indicated that the Norrish–Yang reaction is less probable for one of the two molecules. For the other molecule, the intramolecular geometrical parameters showed that except for the Norrish–Yang reaction, the concurrent reaction leading to the formation of a five-membered ring can also proceed. In (3), both o-isopropyl groups are able to react; however, the bigger volume of a void near 2-isopropyl may be the factor determining the reactivity. For (4), only one o-isopropyl should be reactive.

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.

Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase–cyanocobalamin complex

1999 ◽  
Vol 55 (4) ◽  
pp. 907-909 ◽  
Author(s):  
Jun Masuda ◽  
Tetsuya Yamaguchi ◽  
Takamasa Tobimatsu ◽  
Tetsuo Toraya ◽  
Kyoko Suto ◽  
...  
Keyword(s):  
Klebsiella Oxytoca ◽  
Crystal Form ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Diol Dehydratase ◽  
Replacement Method

Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and preliminary crystallographic experiments have been performed. The crystals belong to two different space groups, depending on the crystallization conditions. One crystal (form I) belongs to space group P212121 with unit-cell parameters a = 76.2, b = 122.3, c = 209.6 Å, and diffracts to 2.2 Å resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to space group P21 with unit-cell parameters a = 75.4, b = 132.7, c = 298.8 Å, β = 91.9°, and diffracts to 3.0 Å resolution. For the purpose of structure determination, a heavy-atom derivative search was carried out and some mercuric derivatives were found to be promising. Structure analysis by the multiple isomorphous replacement method is now under way.

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