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.

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].

Kupfer(I)-chlorid-Addukte von Phosphoraniminen Die Kristallstrukturen von Ph 3 PNPh * CuCl und von 2,3-Bis(triphenylphosphoranylidenamino)maIeinsäure-N-methylimid- Kupfer(I)-chlorid / Copper(I) Chloride Adducts of Phosphoranimines The Crystal Structures of Ph3 PNPh·CuCl and of 2,3-Bis(triphenylphosphoranylideneamino)maleic Acid N-Methylimide Copper(I) Chloride

1988 ◽  
Vol 43 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Andrea Maurer ◽  
Dieter Fenske ◽  
Johannes Beck ◽  
Joachim Strähle ◽  
Eberhard Böhm ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ir Spectra ◽  
Crystal Structures ◽  
Maleic Acid ◽  
Bond Angle ◽  
Asymmetric Unit ◽  
Space Group ◽  
Bond Lengths ◽  
Structure Determinations ◽  
Independent Molecules

Abstract The title compounds Ph3PNPh · CuCl (1) and (Ph3P)2 N2 C4O2 (NMe) CuCl (2) have been prepared by the reactions of CuCl with the corresponding phosphoranimines Ph3PNPh and 2.3-bis(triphenylphosphoranylideneamino)maleic acid N-methylimide, respectively. Both com-plexes were characterized by their IR spectra as well as by crystal structure determinations. Ph3PNPh · CuCl (1): space group P1, Z = 4, 3639 independent observed reflexions, R = 0.038. Lattice dimensions (18 °C): a = 1047.6; b = 1251.5; c = 1755 pm; α = 103.43°; β = 97.24°; γ = 101.30°. The compound forms monomeric molecules; the asymmetric unit contains two crystallo-graphically independent molecules. The CuCl molecule is bonded via the N atom of the phos-phoranimine. Bond lengths: Cu-N = 189 pm; Cu-CI = 209 pm; bond angle N - Cu - CI = 177°. (Ph3P)2N2C4O2(NMe) · CuCl (2): space group Pbca, Z = 8, 5611 independent, observed reflexions, R = 0.069. Lattice dimensions (25 °C): a = 1224.3; b = 1962.5: c = 2994.0 pm. The compound forms monomeric molecules with the CuCl molecule bonded via one of the N atoms of the phosphoranimine groups. Bond lengths: Cu - N = 194 pm; Cu-CI = 212 pm; bond angle N-Cu -CI -175°.

scholarly journals Crystal structures of 2-[3,5-bis(bromomethyl)-2,4,6-triethylbenzyl]isoindoline-1,3-dione and 2-{5-(bromomethyl)-3-[(1,3-dioxoisoindolin-2-yl)methyl]-2,4,6-triethylbenzyl}isoindoline-1,3-dione

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Manuel Stapf ◽  
Betty Leibiger ◽  
Anke Schwarzer ◽  
Monika Mazik
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Molecular Conformation ◽  
Halogen Bond ◽  
Asymmetric Unit ◽  
Space Group ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions

The title compounds, C23H25Br2NO2 (1) and C31H29BrN2O4 (2), crystallize in the space group P21/n with two (1-A and 1-B) and one molecules, respectively, in the asymmetric unit of the cell. The molecular conformation of these compounds is stabilized by intramolecular C—H...O hydrogen bonds and C—H...N or C—H...π interactions. The crystal structure of 1 features a relatively strong Br...O=C halogen bond, which is not observed in the case of 2. Both crystal structures are characterized by the presence of C—H...Br hydrogen bonds and numerous intermolecular C—H...O hydrogen-bonding interactions.

35CI NQR and Structural Studies of N-(2,6-Dichlorophenyl)-Amides, 2,6-Cl2C6H3-NHCO-R (R = H or CH3-y Xy and X = CH3 or CI; y = 0,1, 2 or 3)

2000 ◽  
Vol 55 (9-10) ◽  
pp. 791-800 ◽  
Author(s):  
B. Thimme Gowda ◽  
Helmut Paulus ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Crystal Symmetry ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Space Group ◽  
Lattice Constants ◽  
Bond Lengths ◽  
Crystal Type

The effect of side chain substitution on the 35CI NQR and crystal structure of amides of the type N-(2,6-dichlorophenyl)-amides, 2,6-Cl2C6H3-NHCO-R (R = H or CH3_yXy where X = CH3 or CI and y = 0, 1, 2 or 3), has been studied by measuring the 35C1 NQR spectra and determining the crystal structures of the compounds N-(2,6-dichlorophenyl)-formamide, 2,6-Cl2C6H3- NHCO-H (DCPFA); N-(2,6-dichlorophenyl)-2-methylacetamide(propionamide), 2,6-Cl2C6H3- NHCO-CH2CH3 (DCPMA); N-(2,6-dichlorophenyl)-2,2-dimethylacetamide(isobutyramide), 2,6- Cl2C6H3-NHCO-CH(CH3 ) 2 (DCPDMA) and N-(2,6-dichlorophenyl)-2,2,2-trimethylacetamide (neopentylamide), 2,6-Cl2C6H3-NHCO-C(CH3)3 (DCPTMA), and by analysing the present data along with the 35CI NQR spectra and / or crystal structures of the compounds, 2,6-dichloroaniline, 2,6-Cl2C6H3-NH2 (DCA), N-(2,6-dichlorophenyl)-acetamide, 2,6-Cl2C6H3--NHCO-CH3 (DCPA), N-(2,6-dichlorophenyl)-2-chloroacetamide, 2,6-Cl2C6H3-NHCO-CH2Cl (DCPCA), N- (2,6-dichlorophenyl)-2,2-dichloroacetamide, 2,6-Cl2C6H3-NHCO-CHCl2 (DCPDCA) and N- (2,6-dichlorophenyl)-2,2,2-trichloroacetamide, 2,6-Cl2C6H3-NHCO-CCl3 (DCPTCA). The crystal type, space group, formula units and lattice constants in A of the new structures are;DCPFA: orthorhombic, Pbca, Z = 8, a = 8.593(3), b = 12.728(4), c = 14.376(4); DCPMA: orthorhombic, P212121, Z = 4, a = 4.774(2), b = 10.961(5), c = 19.562(8); DCPDMA: monoclinic, P21/c, Z = 4, a = 9.901(4), b = 13.785(5), c = 9.060(3), ß = 103.58(2)° and DCPTMA: monoclinic, P21/n, Z = 8, a = 16.047(5), b = 9.882(3), c = 16.270(5) ß = 102.12(1)°. The compound, DCPTMA shows two molecules in its asymmetric unit. This is in agreement with the multiple lines observed in the 35CI NQR spectra of the compound. The conversion of DCA (monoclinic) into it's various acid amides DCPFA, DCPA, DCPMA, DCPDMA, DCPTMA, DCPCA and DCPTCA affects it's crystal symmetry. The replacement of the side chain CH3 in DCPA by the H atom or substitution of either a CH3 group or a CI atom for one of the H atoms in the side chain CH3 or replacement of the two ring CI atoms by the H atoms changes it's crystal symmetry from monoclinic to orthorhombic, while the substitution of 2 or all the 3 H atoms in the CH3 group of DCPA by 2 or 3 CH3 groups or CI atoms restores it's crystal symmetry back to the monoclinic type. The bond lengths and bond angles are normal except for some deviations.

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.

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.

Studies in aryltin chemistry. Part 6. Crystal and molecular structures of tetra(p-methylsulphonylphenyl)tin(IV) and tetra(p-methylsulphinylphenyl)tin(IV) monohydrate

1990 ◽  
Vol 68 (8) ◽  
pp. 1277-1282 ◽  
Author(s):  
Ivor Wharf ◽  
Michel G. Simard ◽  
Henry Lamparski
Keyword(s):  
Least Squares ◽  
Crystal Structures ◽  
Direct Method ◽  
Molecular Structures ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Molecular Symmetry ◽  
Asymmetric Unit ◽  
Full Matrix ◽  
Space Group

Tetrakis(p-methylsulphonylphenyl)tin(IV) and tetrakis(p-methylsulphinylphenyl)tin(IV) n-hydrate have been prepared and their spectra (ir 1350–400 cm−1; nmr, 1H, 13C, 119Sn) and X-ray crystal structures are reported. The first compound is monoclinic, space group C2/c, Z = 4, with a = 21.589(6), b = 6.207(3), c = 22.861(11) Å, β = 93.80(3)° (22 °C); the structure was solved by the direct method and refined by full-matrix least squares calculations to R = 0.043 for 2755 observed reflections. It has 2 molecular symmetry with the methyl group and one oxygen atom completely disordered in both CH3S(O2) groups in the asymmetric unit. The second compound is tetragonal, space group P42/n, Z = 2, with a = b = 15.408(6), c = 6.379(2) Å (−100 °C); the structure was solved by the Patterson method and refined by full-matrix least squares calculations to R = 0.060 for 1209 observed reflections. It has [Formula: see text] molecular symmetry with the whole asymmetric unit disordered. Water molecules occupy positions on parallel 42 axes but molecular packing requirements prevent all sites having 100% occupancy giving n ~ 1 for the hydrate. Keywords: Tetra-aryltins, crystal structures, sulphone, sulphoxide, hydrogen-bonding.

Supramolecular assembling using synthons with NH—CO(S)—CS—NH and NH—CO—CO—NH functionalities: crystal structures of (S,S)-N,N′-monothiooxalyldileucine methyl ester and its dithio analogue

2004 ◽  
Vol 60 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Biserka Kojić-Prodić ◽  
Berislav Perić ◽  
Zoran Štefanić ◽  
Anton Meden ◽  
Janja Makarević ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Methyl Ester ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Bond Network ◽  
Bonding Systems

To compare the structural properties of oxalamide and thiooxalamide groups in the formation of hydrogen bonds suitable for supramolecular assemblies a series of retropeptides was studied. Some of them, having oxalamide bridges, are gelators of organic solvents and water. However, retropeptides with oxygen replaced by the sp 2 sulfur have not exhibited such properties. The crystal structures of the two title compounds are homostructural, i.e. they have similar packing arrangements. The monothio compound crystallizes in the orthorhombic space group P212121 with two molecules in the asymmetric unit arranged in a hydrogen-bond network with an approximate 41 axis along the crystallographic b axis. However, the dithio and dioxo analogues crystallize in the tetragonal space group P41 with similar packing patterns and hydrogen-bonding systems arranged in agreement with a crystallographic 41 axis. Thus, these two analogues are isostructural having closely related hydrogen-bonding patterns in spite of the different size and polarity of oxygen and sulfur which serve as the proton acceptors.

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

Sign in / Sign up

Export Citation Format

Share Document