scholarly journals A new crystal form of GABARAPL2

2021 ◽  
Vol 77 (5) ◽  
pp. 140-147
Author(s):  
Kristen Scicluna ◽  
Grant Dewson ◽  
Peter E. Czabotar ◽  
Richard W. Birkinshaw
Keyword(s):  
Crystal Structure ◽  
Type A ◽  
Crystal Form ◽  
Light Chains ◽  
Docking Site ◽  
Asymmetric Unit ◽  
Autophagosome Formation ◽  
Space Group ◽  
Associated Proteins ◽  
Crystal Contact

The Atg8 protein family comprises the GABA type A receptor-associated proteins (GABARAPs) and microtubule-associated protein 1 light chains 3 (MAP1LC3s) that are essential mediators of autophagy. The LC3-interacting region (LIR) motifs of autophagy receptors and adaptors bind Atg8 proteins to promote autophagosome formation, cargo recruitment, and autophagosome closure and fusion to lysosomes. A crystal structure of human GABARAPL2 has been published [PDB entry 4co7; Ma et al. (2015), Biochemistry, 54, 5469–5479]. This was crystallized in space group P21 with a monoclinic angle of 90° and shows a pseudomerohedral twinning pathology. This article reports a new, untwinned GABARAPL2 crystal form, also in space group P21, but with a 98° monoclinic angle. No major conformational differences were observed between the structures. In the structure described here, the C-terminal Phe117 binds into the LIR docking site (LDS) of a neighbouring molecule within the asymmetric unit, as observed in the previously reported structure. This crystal contact blocks the LDS for co-crystallization with ligands. Phe117 of GABARAPL2 is normally removed during biological processing by Atg4 family proteases. These data indicate that to establish interactions with the LIR, Phe117 should be removed to eliminate the crystal contact and liberate the LDS for co-crystallization with LIR peptides.

scholarly journals Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

2014 ◽  
Vol 70 (7) ◽  
pp. 854-859
Author(s):  
Makoto Nakabayashi ◽  
Misumi Kataoka ◽  
Masahiro Watanabe ◽  
Kazuhiko Ishikawa
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Pyrococcus Furiosus ◽  
Crystal Form ◽  
Mutant Enzyme ◽  
Monomeric Form ◽  
Asymmetric Unit ◽  
Oligomeric Structure ◽  
Space Group ◽  
Monomer Structure

One of the β-glucosidases fromPyrococcus furiosus(BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space groupP1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability.

2,4-Diamino-6-phenyl-1,3,5-triazin-1-ium nitrate: intriguing crystal structure with high Z′/Z′′ and hydrogen bond numbers and Hirshfeld surface analysis of intermolecular interactions

CrystEngComm ◽  
2021 ◽  
Author(s):  
Nicoleta Caimac ◽  
Elena Melnic ◽  
Diana Chisca ◽  
Marina S. Fonari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Ionic Species ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Asymmetric Unit ◽  
Space Group

The title compound crystallises in the triclinic centrosymmetric space group P1̄ with an intriguing high number of crystallographically unique binary salt-like adducts (Z′ = 8) and a total number of ionic species (Z′′ = 16) in the asymmetric unit.

scholarly journals 2,2-Difluoro-3-(4-fluorophenyl)-2H-benzo[e][1,3,2]oxazaborinin-3-ium-2-uide

IUCrData ◽  
2017 ◽  
Vol 2 (8) ◽  
Author(s):  
Błażej Dziuk ◽  
Borys Ośmiałowski ◽  
Anna Zakrzewska ◽  
Krzysztof Ejsmont ◽  
Bartosz Zarychta
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Dihedral Angle ◽  
Title Compound ◽  
Independent Molecule ◽  
Asymmetric Unit ◽  
Space Group ◽  
Compound C ◽  
Centrosymmetric Space Group ◽  
Intermolecular Contacts

There is one independent molecule in the asymmetric unit of the title compound, C13H9BF3NO, which crystallizes in the non-centrosymmetric space groupCc. In the molecular structure, the BF2-carrying ring is distorted from planarity and its mean plane makes a dihedral angle of 42.3 (1)° with the 4-fluorophenyl ring. F atoms are involved in all of the short intermolecular contacts of the crystal structure, which link molecules to form chains along [001] and [010].

scholarly journals N′-[(E)-4-Bromobenzylidene]-2-(4-isobutylphenyl)propanohydrazide

2009 ◽  
Vol 65 (6) ◽  
pp. o1184-o1185 ◽  
Author(s):  
Hoong-Kun Fun ◽  
Ching Kheng Quah ◽  
K. V. Sujith ◽  
B. Kalluraya
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Asymmetric Unit ◽  
Higher Symmetry ◽  
Space Group ◽  
Compound C ◽  
Benzene Rings ◽  
Independent Molecules ◽  
Symmetry Space ◽  
Symmetry Space Group

The asymmetric unit of the title compound, C20H23BrN2O, contains two independent molecules (AandB), in which the orientations of the 4-isobutylphenyl units are different. The dihedral angle between the two benzene rings is 88.45 (8)° in moleculeAand 89.87 (8)° in moleculeB. MoleculesAandBare linked by a C—H...N hydrogen bond. In the crystal, molecules are linked into chains running along theaaxis by intermolcular N—H...O and C—H...O hydrogen bonds. The crystal structure is further stabilized by C—H...π interactions. The presence of pseudosymmetry in the structure suggests the higher symmetry space groupPbca. However, attempts to refine the structure in this space group resulted in a disorder model with highR(0.097) andwR(0.257) values. The crystal studied was an inversion twin with a 0.595 (4):0.405 (4) domain ratio.

scholarly journals Synthesis and crystal structure of Na4Ni7(AsO4)6

2016 ◽  
Vol 72 (5) ◽  
pp. 632-634 ◽  
Author(s):  
Rénald David
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
Site Symmetry ◽  
Asymmetric Unit ◽  
Synthesis And Crystal Structure ◽  
Space Group ◽  
Ceramic Synthesis ◽  
The One

The title compound, tetrasodium heptanickel hexaarsenate, was obtained by ceramic synthesis and crystallizes in the monoclinic space groupC2/m. The asymmetric unit contains seven Ni atoms of which two have site symmetry 2/mand three site symmetry 2, four As atoms of which two have site symmetrymand two site symmetry 2, three Na atoms of which two have site symmetry 2, and fifteen O atoms of which four have site symmetrym. The structure of Na4Ni7(AsO4)6is made of layers of Ni octahedra and As tetrahedra assembled in sheets parallel to thebcplane. These layers are interconnected by corner-sharing between NiO6octahedra and AsO4tetrahedra. This linkage creates tunnels running along thecaxis in which the Na atoms are located. This arrangement is similar to the one observed in Na4Ni7(PO4)6, but the layers of the two compounds are slightly different because of the disorder of one of the Ni sites in the structure of the title compound.

scholarly journals Crystal structure of strontium dinickel iron orthophosphate

2015 ◽  
Vol 71 (10) ◽  
pp. 1255-1258 ◽  
Author(s):  
Said Ouaatta ◽  
Abderrazzak Assani ◽  
Mohamed Saadi ◽  
Lahcen El Ammari
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Solid State Reaction ◽  
Title Compound ◽  
Three Dimensional ◽  
The Other ◽  
Asymmetric Unit ◽  
Space Group ◽  
Edge Sharing Octahedra ◽  
Wyckoff Position

The title compound, SrNi2Fe(PO4)3, synthesized by solid-state reaction, crystallizes in an ordered variant of the α-CrPO4structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space groupImma: the Sr cation and one P atom occupy the Wyckoff position 4e(mm2), Fe is on 4b(2/m), Ni and the other P atom are on 8g(2), one O atom is on 8h(m) and the other on 8i(m). The three-dimensional framework of the crystal structure is built up by [PO4] tetrahedra, [FeO6] octahedra and [Ni2O10] dimers of edge-sharing octahedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octahedra ([Ni2O10] dimer) linked to [PO4] tetrahedraviacommon edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetrahedra and FeO6octahedra sharing apices. The layers are held together through vertices of [PO4] tetrahedra and [FeO6] octahedra, leading to the appearance of two types of tunnels parallel to thea- andb-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms.

(Acetylacetonato-κ2O,O′)(2,2′-bipyridine-κ2N,N′)iodidocopper(II): a compound with two molecules in the asymmetric unit due to different π–π interactions

2013 ◽  
Vol 69 (9) ◽  
pp. 1010-1012 ◽  
Author(s):  
Lorrane Diniz ◽  
Sandra Carvalho ◽  
Ruth H. U. Borges ◽  
Bernardo L. Rodrigues
Keyword(s):  
Crystal Structure ◽  
Title Complex ◽  
Asymmetric Unit ◽  
Space Group ◽  
Π Interactions

The crystal structure of the title complex, [Cu(C5H7O2)I(C10H8N2)], in the space groupP\overline{1} withZ= 4, is stabilized by π–π interactions and weak C—H...I interactions. The presence of two molecules in the asymmetric unit is associated with different intermolecular π–π interactions between two symmetry-related molecules of each type.

scholarly journals Synthesis and Crystal Structure of Bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate Showing Three Anion/Cation Couples in the Asymmetric Unit

Crystals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 617 ◽  
Author(s):  
Elisa Fresta ◽  
Marco Milanesio ◽  
Giorgio Volpi ◽  
Claudia Barolo ◽  
Eleonora Conterosito
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Driving Force ◽  
Hirshfeld Surface ◽  
Asymmetric Unit ◽  
Aromatic Rings ◽  
Synthesis And Crystal Structure ◽  
Space Group ◽  
Distorted Octahedral ◽  
Torsional Angles

The title compound bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate, a six-coordinate iridium(III) complex, crystallizes in the P-1 space group. Iridium is in a distorted octahedral (n = 6) coordination with the N,C’ atoms of two phenylpyridine and the N atoms of two acetonitrile ligands. The peculiarity of this structure is that three independent moieties of the title compound and three PF6− anions, to counterbalance the charge, are observed in the asymmetric unit and this is a rather uncommon fact among the Cambridge Crystallographic Database (CSD) entries. The three couples are almost identical conformers with very similar torsional angles. The packing, symmetry, and space group were accurately analyzed and described also by means of Hirshfeld surface analysis, which is able to underline subtle differences among the three anion/cation couples in the asymmetric unit. The driving force of the packing is the clustering of the aromatic rings and the maximization of acetonitrile:PF6− interactions. The asymmetry of the cluster is the cause of the unusual number of moieties in the asymmetric unit.

scholarly journals Crystal structures of two (±)-exo-N-isobornylacetamides

2015 ◽  
Vol 71 (10) ◽  
pp. 1117-1120 ◽  
Author(s):  
Dmitrijs Stepanovs ◽  
Daniels Posevins ◽  
Maris Turks
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Asymmetric Unit ◽  
Double Chain ◽  
Space Group ◽  
Axis Direction ◽  
Independent Molecules

The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO (±)-(1) {systematic name: (±)-N-[(1RS,2RS,4RS)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, and chloroacetamide, C12H20ClNO (±)-(2) {systematic name: (±)-2-chloro-N-[(1RS,2RS,4RS)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of (±)-(1) has been reported previously [Unget al.(2014).Monatsh. Chem.145, 983–992]. Compound (±)-(1) crystallizes in the space groupP21/nwith two independent molecules in the asymmetric unit, in contrast to the above-mentioned polymorph which crystallized in the space groupC2/cwith one molecule in the asymmetric unit. In the title compounds, the bicyclic bornane moieties have normal geometries. In the crystals of both compounds, molecules are linked by N—H...O hydrogen bonds, reinforced by C—H...O contacts, formingtrans-amide chains propagating along thea-axis direction. In the case of compound (±)-(1), neighbouring chains are linked by further C—H...O contacts, forming double-chain ribbons along [100].

THE CRYSTAL STRUCTURE OF 1,4-DIBROMONAPHTHALENE

1961 ◽  
Vol 39 (8) ◽  
pp. 1574-1578 ◽  
Author(s):  
J. Trotter
Keyword(s):  
Crystal Structure ◽  
Detailed Examination ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Space Group ◽  
Bond Lengths ◽  
Sufficient Precision ◽  
Molecular Dimensions

Crystals of 1,4-dibromonaphthalene are monoclinic with eight molecules in a unit cell of dimensions a = 27.45, b = 16.62, c = 4.09 Å; β = 91.9°; space group P21/a The high proportion of bromine in the crystal probably precludes location of the carbon atoms with sufficient precision to give accurate molecular dimensions, and it has therefore not been considered worth while proceeding beyond the detailed examination of the projection along the short c-axis. There are two molecules in the asymmetric unit, and the solution of the structure from hk0 Patterson and Fourier projections has indicated that these two molecules are related, at least in projection, by a pseudo center of symmetry. The projected bond distances indicate significant deviations of the bromine atoms from the aromatic plane. Approximate values of the bond lengths in the molecule have been deduced from the projected distances and estimated orientation angles.

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