Clathrates and semiclathrates of Type-I: crystal structure and superstructures

2013 ◽  
Vol 228 (5) ◽  
pp. 215-227 ◽  
Author(s):  
Maria A. Kirsanova ◽  
Andrei V. Shevelkov
Keyword(s):  
Crystal Structure ◽  
Type I

Crystal structure of magnesium chromium vanadate Mg2CrV3O11, a member of the A2BV3O11 vanadate family

2007 ◽  
Vol 22 (3) ◽  
pp. 246-252 ◽  
Author(s):  
A. Worsztynowicz ◽  
S. M. Kaczmarek ◽  
W. Paszkowicz ◽  
R. Minikayev
Keyword(s):  
Crystal Structure ◽  
Rietveld Method ◽  
Ion Pairs ◽  
Exchange Constant ◽  
Type I ◽  
Type Ii ◽  
Paramagnetic Resonance ◽  
Interatomic Distances ◽  
Electron Paramagnetic ◽  
Full Occupancy

The crystal structure of recently discovered chromium (III) dimagnesium trivanadate (V) Mg2CrV3O11 was refined using the Rietveld method. The crystal system of Mg2CrV3O11 is triclinic with space group P1− (Mg1.7Zn0.3GaV3O11 type) and lattice parameters a=6.4057(1) Å, b=6.8111(1) Å, c=10.0640(2) Å, α=97.523(1)°, β=103.351(1)°, γ=101.750(1)°, and Z=2. The characteristic feature of compounds in the A2BV3O11 (A=Mg, Zn and B=Ga, Fe, Cr) family is a strong tendency to share the octahedral M(1) and M(2) sites by both divalent A and trivalent B atoms, and the bipyramidal M(3) sites occupied by divalent A ions. In the present refinement, the only constraint assuming full occupancy of the M(1), M(2), and M(3) sites leads to the following Cr/(Cr+Mg) ratios: 0.70(2) at M(1), 0.24(2) at M(2), and 0.03(2) at M(3). These occupancies are discussed and compared to those of isotypic compounds. The values of interatomic distances are found to be comparable with those reported by R. D. Shannon in 1976. Electron paramagnetic resonance has been also analyzed. Two absorption lines with g≈2.0 (type I) and g≈1.98 (type II) have been recorded in the EPR spectra, and attributed to V4+ ions and Cr3+–Cr3+ ion pairs, respectively. The exchange constant J between Cr3+ ions has been calculated.

Synthesis, Crystal Structure, and Physical Properties of the Type-I Clathrate Ba8−δNix□ySi46–x–y

2012 ◽  
Vol 51 (8) ◽  
pp. 4730-4741 ◽  
Author(s):  
U. Aydemir ◽  
C. Candolfi ◽  
A. Ormeci ◽  
H. Borrmann ◽  
U. Burkhardt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Physical Properties ◽  
Type I

scholarly journals The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin β by endogenous fetuin-B

2021 ◽  
Vol 118 (14) ◽  
pp. e2023839118
Author(s):  
Ulrich Eckhard ◽  
Hagen Körschgen ◽  
Nele von Wiegen ◽  
Walter Stöcker ◽  
F. Xavier Gomis-Rüth
Keyword(s):  
Crystal Structure ◽  
Glycan Structure ◽  
Type I ◽  
Zinc Ions ◽  
Transmembrane Segment ◽  
Protein Inhibitor ◽  
Catalytic Domains ◽  
Endogenous Protein ◽  
Switch Mechanism ◽  
Catalytic Zinc

Meprin β (Mβ) is a multidomain type-I membrane metallopeptidase that sheds membrane-anchored substrates, releasing their soluble forms. Fetuin-B (FB) is its only known endogenous protein inhibitor. Herein, we analyzed the interaction between the ectodomain of Mβ (MβΔC) and FB, which stabilizes the enzyme and inhibits it with subnanomolar affinity. The MβΔC:FB crystal structure reveals a ∼250-kDa, ∼160-Å polyglycosylated heterotetrameric particle with a remarkable glycan structure. Two FB moieties insert like wedges through a “CPDCP trunk” and two hairpins into the respective peptidase catalytic domains, blocking the catalytic zinc ions through an “aspartate switch” mechanism. Uniquely, the active site clefts are obstructed from subsites S4 to S10′, but S1 and S1′ are spared, which prevents cleavage. Modeling of full-length Mβ reveals an EGF-like domain between MβΔC and the transmembrane segment that likely serves as a hinge to transit between membrane-distal and membrane-proximal conformations for inhibition and catalysis, respectively.

Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding

2010 ◽  
Vol 391 (1) ◽  
Author(s):  
Renu Batra-Safferling ◽  
Joachim Granzin ◽  
Susanne Mödder ◽  
Silke Hoffmann ◽  
Dieter Willbold
Keyword(s):  
Crystal Structure ◽  
Ligand Binding ◽  
Protein Interactions ◽  
Intracellular Signaling ◽  
Sh3 Domain ◽  
Peptide Ligand ◽  
Type I ◽  
Phosphatidylinositol 3 Kinase ◽  
Anchor Residue ◽  
Phosphatidylinositol 3

Abstract Src homology 3 (SH3) domains are mediators of protein-protein interactions. They comprise approximately 60 amino acid residues and are found in many intracellular signaling proteins. Here, we present the crystal structure of the SH3 domain from phosphatidylinositol 3-kinase (PI3K) in complex with the 12-residue proline-rich peptide PD1R (HSKRPLPPLPSL). The crystal structure of the PI3K SH3-PD1R complex at a resolution of 1.7 Å reveals type I ligand orientation of the bound peptide with an extended conformation where the central portion forms a left-handed type II polyproline (PPII) helix. The overall structure of the SH3 domain shows minimal changes on ligand binding. In addition, we also attempted crystallization with another peptide ligand (PD1) where the residue at anchor position P-3 is a tyrosine. The crystals obtained did not contain the PD1 ligand; instead, the ligand binding site is partially occupied by residues Arg18 and Trp55 from the symmetry-related PI3K SH3 molecule. Considering these crystal structures of PI3K SH3 together with published reports, we provide a comparative analysis of protein-ligand interactions that has helped us identify the individual residues which play an important role in defining target specificity.

scholarly journals Crystal structure of the adenosine A2Areceptor bound to an antagonist reveals a potential allosteric pocket

2017 ◽  
Vol 114 (8) ◽  
pp. 2066-2071 ◽  
Author(s):  
Bingfa Sun ◽  
Priti Bachhawat ◽  
Matthew Ling-Hon Chu ◽  
Martyn Wood ◽  
Tom Ceska ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Protein Structures ◽  
Binding Pocket ◽  
Cubic Phase ◽  
Receptor Subtype ◽  
Type I ◽  
Intracellular Loop ◽  
Drug Candidates

The adenosine A2Areceptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2Areceptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyld-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2Areceptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.

scholarly journals Symmetrical Noncovalent Interactions Br···Br Observed in Crystal Structure of Exotic Primary Peroxide

Symmetry ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 637 ◽  
Author(s):  
Dmitrii S. Bolotin ◽  
Mikhail V. Il’in ◽  
Vitalii V. Suslonov ◽  
Alexander S. Novikov
Keyword(s):  
Crystal Structure ◽  
Quantum Theory ◽  
Solid State ◽  
Single Crystal ◽  
Quantum Chemical ◽  
Driving Forces ◽  
Weak Interactions ◽  
Noncovalent Interactions ◽  
Type I ◽  
Single Crystal Xrd

4-Bromobenzamidrazone reacts with cyclopentanone giving 3-(4-bromophenyl)-5-(4-peroxobutyl)-1,2,4-triazole, which precipitated as pale-yellow crystals during the reaction. The intermolecular noncovalent interactions Br···Br in the single-crystal XRD structure of the peroxo compound were studied theoretically using quantum chemical calculations (ωB97XD/x2c-TZVPPall) and quantum theory of atoms in molecules (QTAIM) analysis. These attractive intermolecular noncovalent interactions Br···Br is type I halogen···halogen contacts and their estimated energy is 2.2–2.5 kcal/mol. These weak interactions are suggested to be one of the driving forces (albeit surely not the main one) for crystallization of the peroxo compound during the reaction and thus its stabilization in the solid state.

Powder XRD and TEM study on crystal structure and interstratification of Zn-chlorite (baileychlore)

2017 ◽  
Vol 32 (2) ◽  
pp. 118-123 ◽  
Author(s):  
Seungyeol Lee ◽  
Huifang Xu
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Analytical Electron Microscopy ◽  
Type I ◽  
Octahedral Sheet ◽  
X Ray ◽  
Cell Parameters ◽  
Reitveld Refinement ◽  
Calcite Veins ◽  
Stacking Disorder

Baileychlore is Zn-end member trioctahedral chlorite, named by Audrey C. Rule and Frank Radke in 1988 for the honor of Professor Sturges W. Bailey of the University of Wisconsin – Madison, USA. Baileychlore occurs as dark green chlorite on calcite veins from garnet-vesuvianite skarn clasts at Red Dome ore deposit, Chillagoe, Queensland, Australia. The baileychlore has been studied by using powder X-ray diffraction (XRD), transmission electron microscopy (TEM), and X-ray energy-dispersive analytical electron microscopy analyses to determine crystal structure and interstratified layers. Baileychlore with stacking disorder displays streaking reflections of 0k0 (≠6n) hhl (h ≠ 3n). Unit-cell parameters for baileychlore (type I polytype) with a space group of C$ \bar 1$ are: a = 5.351(3), b = 9.266(5), c = 14.418(8) Å, α = 89.741(3)°, β = 96.741(4)°, and γ = 90.122(2)°. The strong lines of the measured XRD pattern [d(Å)(I)(hkl)] are: 14.331(7.151)(90.5)(002); 4.574(23.2)(1$ \bar 1$0, 11$ \bar 1$); 3.572(38.5)(004); 2.653(31.4)($ \bar 1$31, 200, 13$ \bar 1$); 2.406(49.4)(202, $ \bar 1$33, 13$ \bar 3$); 1.543(27.6)($ \bar 3$31, 060, 33$ \bar 1$), respectively. Reitveld refinement provides a composition (Zn2.49Al0.09Fe2+ 0.09□0.33)0.61− for the octahedral sheet and (Si3.53Al0.47)0.47− for the tetrahedral sheets within the 2:1 layer with (Al1.08Fe1.08Mg0.84)1.08+ for the interlayer sheet. The refinement results indicate that baileychlore is an intergrowth of type I and II polytypes. High-resolution TEM images show stacking disorder of baileychlore with small amount of isolated smectite layers.

scholarly journals Insights into substrate binding and catalysis in bacterial type I dehydroquinase

2014 ◽  
Vol 462 (3) ◽  
pp. 415-424 ◽  
Author(s):  
María Maneiro ◽  
Antonio Peón ◽  
Emilio Lence ◽  
José M. Otero ◽  
Mark J. Van Raaij ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Binding ◽  
Detailed Knowledge ◽  
Type I ◽  
Conserved Residues ◽  
Binding Process ◽  
Bacterial Type

The crystal structure of S. typhi type I dehydroquinase in complex with (2R)-3-methyl-3-dehydroquinic acid is described. A previously unknown key role of several conserved residues and a detailed knowledge of the substrate binding process is detailed.

Crystal structure of modulated martensite and crystallographic correlations between martensite variants of Ni50Mn38Sn12alloy

2016 ◽  
Vol 49 (4) ◽  
pp. 1276-1283 ◽  
Author(s):  
Chunqing Lin ◽  
Haile Yan ◽  
Yudong Zhang ◽  
Claude Esling ◽  
Xiang Zhao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Backscatter Diffraction ◽  
Type I ◽  
Type Ii ◽  
Plate Interface ◽  
Modulated Structure ◽  
Austenite Grain ◽  
Twinning Plane ◽  
Backscatter Diffraction ◽  
Comprehensive Study

A comprehensive study on the crystal structure, the microstructure and the crystallographic features of the martensite in an Ni50Mn38Sn12alloy has been conducted in the present work. The results show that the martensite possesses a 4O modulated structure. The martensite is organized into broad plates in the original austenite grain. The plates contain irregularly shaped colonies with two characteristic microstructural patterns: a classical lamellar pattern and a herringbone pattern. Crystallographic analyses by scanning electron microscopy/electron backscatter diffraction demonstrate that in each colony there are four orientation variants (A, B, C and D) and they form three types of twins (type I, type II and compound twin). The interfaces between corresponding variants are coincident with their twinning planeK1. The interface planes of the compound twin pairs A&D and B&C can have one or two different orientations, which leads to the two microstructural patterns. The corresponding variants in neighboring colonies within one broad plate (intra-plate colonies) possess close orientations, but the type I and the type II twin relationships are interchanged. The variants in neighboring colonies situated in adjacent plates (inter-plate colonies) are type I or type II twin related but with some angular deviations. The plate interface is defined by the {221} plane of the variant pair with largest thickness. The results of the present work provide comprehensive microstructural and crystallographic information on modulated martensite in NiMnSn alloys that is useful for the understanding of their specific functionalities and helpful for further investigation on property optimization of these materials.

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