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 Purification, crystallization and preliminary crystallographic analysis of DR0248, an MNT–HEPN fused protein fromDeinococcus radiodurans

2015 ◽  
Vol 71 (1) ◽  
pp. 49-53
Author(s):  
Gaelle Pesce ◽  
Simone Pellegrino ◽  
Sean McSweeney ◽  
AnaMaria Goncalves ◽  
Daniele de Sanctis
Keyword(s):  
Deinococcus Radiodurans ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
Nucleotide Binding Domain ◽  
Unit Cell Parameters ◽  
Dodecyldimethylamine Oxide ◽  
Space Group ◽  
Cell Parameters ◽  
Nucleotidyl Transferase

DR0248 is a protein identified in theDeinococcus radiodurans(DR) genome that is predicted to encompass two domains: an N-terminal minimal nucleotidyl transferase domain (MNT) and a C-terminal higher eukaryotes and prokaryotes nucleotide-binding domain (HEPN). These two domains, usually encoded in two ORFs, have been suggested to play the role of a toxin–antitoxin (TA) system in prokaryotes. Recombinant DR0248 was overexpressed and purified fromEscherichia coliand diffraction-quality crystals were obtained in the presence of the detergent molecules dodecyldimethylamine oxide (DDAO) and octaethylene glycol monododecyl ether (C12E8), which were used as crystallization additives. Crystals grown with DDAO diffracted to a resolution of 2.24 Å and belonged to space groupC2221, with unit-cell parametersa= 98.4,b= 129.9,c= 59.2 Å. Crystals grown with C12E8 diffracted to a resolution of 1.83 Å and belonged to space groupP212121, with unit-cell parametersa= 51.6,b= 87.2,c= 108.2 Å. The structure was solved by multiwavelength anomalous dispersion from zinc bound to the protein using a single crystal obtained in the presence of DDAO.

scholarly journals Cloning, expression, crystallization and crystallographic analysis of CouR fromRhodopseudomonas palustris

2015 ◽  
Vol 71 (11) ◽  
pp. 1416-1420 ◽  
Author(s):  
Chen Pan ◽  
Yong-lin Hu ◽  
Xiang-ning Jiang ◽  
Ying Gai
Keyword(s):  
Rhodopseudomonas Palustris ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Ligand Complex ◽  
Space Group ◽  
Cell Parameters ◽  
Dna Fragment

CouR fromRhodopseudomonas palustrisis a member of the MarR transcriptional regulator family. It regulates the expression of CouA and CouB, enzymes that are involved in the degradation ofp-coumarate.In vivo, CouR binds to a DNA fragment containing thecouABpromoter and suppresses the expression of CouA and CouB, while binding ofp-coumaroyl-CoA attenuates its affinity towards DNA and activates the expression of CouA and CouB. Here, the crystallization and X-ray diffraction analyses of CouR alone and in complex withp-coumaroyl-CoA are reported. Apo and ligand-complexed CouR crystals diffracted to 2.5 and 3.3 Å resolution, respectively. The crystals of apo CouR belonged to space groupP22121, with unit-cell parametersa= 62.78,b = 76.15,c = 87.38 Å, whereas the crystals of the CouR–ligand complex belonged to space groupP212121, with unit-cell parametersa= 61.37,b= 69.82,c = 70.32 Å. The crystals were predicted to contain two CouR molecules or CouR–ligand complexes per asymmetric unit.

scholarly journals Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase fromZymomonas mobilis

2016 ◽  
Vol 72 (3) ◽  
pp. 172-178
Author(s):  
Aili Zhang ◽  
Erhong Guo ◽  
Lanfang Qian ◽  
Nga-Yeung Tang ◽  
Rory M. Watt ◽  
...  
Keyword(s):  
Analytical Ultracentrifugation ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
Wild Type Enzyme ◽  
Unit Cell Parameters ◽  
Inorganic Polyphosphate ◽  
Space Group ◽  
Cell Parameters ◽  
External Stresses ◽  
Similar Unit

Exopolyphosphatase (PPX) enzymes degrade inorganic polyphosphate (poly-P), which is essential for the survival of microbial cells in response to external stresses. In this study, a putative exopolyphosphatase fromZymomonas mobilis(ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space groupC2, with unit-cell parametersa= 122.0,b= 47.1,c= 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule was identified per asymmetric unit. Analytical ultracentrifugation confirmed that ZmPPX forms a dimer in solution. It was confirmed that ZmPPX possesses exopolyphosphatase activity against a synthetic poly-P substrate.

Crystallization of the N-terminal domain of the Escherichia coli regulatory protein TyrR

1999 ◽  
Vol 55 (11) ◽  
pp. 1923-1924 ◽  
Author(s):  
Kirsty H. R. MacPherson ◽  
Paul D. Carr ◽  
Denis Verger ◽  
Terry Kwok ◽  
Barrie E. Davidson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Weight ◽  
Regulatory Protein ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Terminal Domain

The N-terminal domain of the regulatory protein TyrR from Escherichia coli forms a dimer in solution and has been purified and crystallized. The crystals belong to space group C2 with unit-cell parameters a = 134.5, b = 72.1, c = 96.7 Å, β = 98.5°. The crystals diffract to 2.8 Å. Assuming a molecular weight of 23219 Da, a Vm of 2.5 Å3 Da−1 is obtained for two dimers in the asymmetric unit.

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.

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.

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