Crystallographic Threefold Axis Research Articles

Higher-order structure formation using refined monomer structures of lipid raft markers, Stomatin, Prohibitin, Flotillin, and HflK/C-related proteins.

Currently, information on the higher-order structure of Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH)-domain proteins is limited. Briefly, the coordinate information (Refined PH1511.pdb) of the stomatin ortholog, PH1511 monomer, was obtained using the artificial intelligence, ColabFold: AlphaFold2. Thereafter, the 24mer homo-oligomer structure of PH1511 was constructed using the superposing method, with HflK/C and FtsH (KCF complex) as templates. The 9mer-12mer homo-oligomer structures of PH1511 were also constructed using the ab initio docking method, with the GalaxyHomomer server for artificiality elimination. The features and functional validity of the higher-order structures were discussed. The coordinate information (Refined PH1510.pdb) of the membrane protease PH1510 monomer, which specifically cleaves the C-terminal hydrophobic region of PH1511, was obtained. Thereafter, the PH1510 12mer structure was constructed by superposing 12 molecules of the Refined PH1510.pdb monomer onto a 1510-C prism-like 12mer structure formed along the crystallographic threefold helical axis. The 12mer PH1510 (prism) structure revealed the spatial arrangement of membrane-spanning regions between the 1510-N and 1510-C domains within the membrane tube complex. Based on these refined 3D homo-oligomeric structures, the substrate recognition mechanism of the membrane protease was investigated. These refined 3D homo-oligomer structures are provided via PDB files as Supplementary data and can be used for further reference.

Synthesis and structure determination of racemic (Δ/Λ)-tris-(ethyl-enedi-amine)-cobalt(III) trichloride hemi(hexa-aqua-sodium chloride).

The synthesis and crystal structure of the title racemic compound, [Co(C2H8N2)3]Cl3.{[Na(H2O)6]Cl}0.5, are reported. The trivalent cobalt atom, which resides on a crystallographic threefold axis, is chelated by a single ethyl-ene di-amine (en) ligand and yields the tris-chelate [Co(en)3]3+ cation with distorted octa-hedral geometry after the application of crystal symmetry. The sodium cation (site symmetry ), has a single water mol-ecule bound to it in the asymmetric unit and yields a distorted, octa-hedrally coordinated hydrated [Na(H2O)6]+ cation after the application of symmetry. One of the chloride ions lies on a general position and the other has site symmetry. An extensive array of C-H⋯O, N-H⋯Cl and O-H⋯Cl hydrogen bonds exists between the ethyl-ene di-amine ligands, the water mol-ecules of hydration, and the anions present, thereby furnishing solid-state stability.

Heterometallic CoII-CoIII-MII alkoxido-bridged heptanuclear motifs (M = Cu, Zn). Syntheses, crystal structures and magnetic properties

Abstract Two new alkoxido-bridged heterometallic complexes of formula [CoIICoIII3CuII3(dea)6(CH3COO)3](ClO4)0.75(CH3COO)1.25 (1) and [CoII2CoIII2ZnII3(tea)2(piv)6(CH3O)2(OH)2(CH3OH)2]·H2O 2 (H2dea = diethanolamine, H3tea = triethanolamine and Hpiv = pivalic acid) have been assembled using aminoalcohol ligands. The cationic core in 1 possesses a threefold crystallographic axis, and it exhibits a set of three copper(II), one cobalt(II) and three cobalt(III) ions arranged as a hexagon of alternating copper(II) and cobalt(III) ions around the central cobalt(II) ion. Each edge of the hexagon is defined by a double alkoxido bridge, the outer one being bis-monodentate with copper(II)-cobalt(III) pair whereas the inner one adopts a tris-monodentate coordination mode linking the Cu(II)-Co(III) pair with the central cobalt(II) ion. The acetate groups act as bidentate ligands towards the copper(II) ions. The intramolecular cobalt(II)-copper(II) separation is 3.157 A. A hexagon of two cobalt(II), two cobalt(II) and two zinc(II) ions distributed along three types of edges with a central zinc(II) ion occurs in 2. A tris-modentate alkoxido bridge is involved in all edges together with another bis-monodentate alkoxido bridge (CoIII-CoII and CoII-ZnII pairs) and a carboxylate-pivalate bridge in the syn-syn conformation. The five coordination at each peripheral zinc(II) ion is completed by a monodentate carboxylate-pivalate ligand whereas a methoxo group allows to achieve the six-coordination at each cobalt(III) ion. The intramolecular cobalt(II)-cobalt(II) separation through the inner zinc(II) ion is 6.309 A. The magnetic properties of 1 and 2 have been investigated in the temperature range 1.9–300 K. The exchange interaction between the six-coordinate cobalt(II) and copper(II) ions through the double alkoxido bridges in 1 and that between the six-coordinate cobalt(II) ions across the diamagnetic zinc(II) ion in 2 are found to be ferromagnetic [J = +5.39(5) (1) and +1.05(2) cm−1 (2)], the accidental orthogonality between the interacting magnetic orbitals accounting for this behaviour in the two cases.

At last! The single-crystal X-ray structure of a naturally occurring sample of the ilmenite-type oxide FeCrO3.

A natural single crystal of the ferrimagnetic oxide FeCrO3, which was found in an opencast mine situated in the San Luis Potosí State in Mexico, has been characterized in order to elucidate some outstanding issues about the actual structure of this material. The single-crystal X-ray analysis unambiguously shows that transition metal cations are segregated in alternating layers normal to the threefold crystallographic axis, affording a structure isomorphous to that of ilmenite (FeTiO3), in the space group R3̅. The possible occurrence of cation antisite and vacancy defects is below the limit of detection available from X-ray data. Structural and magnetic results are in agreement with the coherent slow intergrowth of magnetic phases provided by the two antiferromagnetic corundum-type parent oxides Fe2O3 (hematite) and Cr2O3 (eskolaite). Our results are consistent with the most recent density functional theory (DFT) studies carried out on digital FeCrO3 [Sadat Nabi & Pentcheva (2011). Phys. Rev. B, 83, 214424], and suggest that synthetic samples of FeCrO3 might present a cation distribution different to that of the ilmenite structural type.

Crystal structure of tris-(1,3-dimesityl-4,5-di-hydro-1H-imidazol-3-ium) tetra-bromido-cobaltate(II) bromide chloro-form hexa-solvate.

In the unit cell of the title compound, (C21H27N2)3[CoBr4]Br·6CHCl3, the tetrabromidocobaltate(II) anion and the bromide anion are located on a crystallographic threefold rotation axis. For the [CoBr4]2− group, the axis runs through one of the Br ligands and the CoII atom. All other structure moieties lie on general sites. Various tris­(1,3-dimesityl-4,5-di­hydro-1H-imidazol-3-ium) structures with different counter-ions have been reported. In the title compound, the N—C—N angle is 113.7 (5)°, with short C—N bond lengths of 1.297 (7) and 1.307 (7) Å. The two mesityl planes make a dihedral angle of 34.6 (1)° and the dihedral angles between the mesityl and N–C–N planes are 82.0 (1) and 88.5 (1)°, respectively. The imidazoline ring is almost planar, with atom deviations in the range 0.003 (5)–0.017 (5) Å from the best plane; the mean deviation is 0.012 (5) Å. In the crystal, non-covalent inter­actions of the C—H⋯Br type occur between the Br− anion and the cation, as well as between the [CoBr4]2− anion and both the chloro­form solvent mol­ecules. These H⋯A distances are slightly shorter than the sum of van der Waals radii.

Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA).

Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes a reversible reaction for adding an O-acyl group to the GlcNAc in UDP-GlcNAc in the first step of lipid A biosynthesis. Lipid A constitutes a major component of lipopolysaccharides, also referred to as endotoxins, which form the outer monolayer of the outer membrane of Gram-negative bacteria. Ligand-free and UDP-GlcNAc-bound crystal structures of LpxA from Bacteroides fragilis NCTC 9343, the most common pathogenic bacteria found in abdominal abscesses, have been determined and are presented here. The enzyme crystallizes in a cubic space group, with the crystallographic threefold axis generating the biological functional homotrimer and with each monomer forming a nine-rung left-handed β-helical (LβH) fold in the N-terminus followed by an α-helical motif in the C-terminus. The structure is highly similar to LpxA from other organisms. Yet, despite sharing a similar LβH structure with LpxAs from Escherichia coli and others, previously unseen calcium ions are observed on the threefold axis in B. fragilis LpxA to help stabilize the trimeric assembly.

Pseudo-symmetry, rotation- and inversion-twinning of a structure with dinuclear and trinuclear Cd complexes. CP-MAS-NMR and IR spectroscopies characterisation

The structure of the complex [C18H30Cd3Cl6N18S12·2(C18H30Cd2Cl3N18S12)·CdCl4], or [L6Cd3Cl6·2(L6Cd2Cl3)·CdCl4], with L being 2-amino-5-(methylthio)-1,3,4-thiadiazole, C3H5N3S2, crystallizes in the trigonal polar space group R3. The crystal packing features three chemically distinct cadmium complex species with eight crystallographically independent Cd(II) ions distributed over two types of L ligand complexes with two and three Cd(II) centers, respectively, and a tetrachlorocadmate(II) ion. The coordination environment of the cadmium ions in the dinuclear and trinuclear complexes is a distorted octahedron. The tetrachlorocadmate(II) is disordered around a crystallographic threefold rotation axis, which is, in turn, inducing disorder onto the two methyl-thio groups in closest proximity to a CdCl4anion. The crystal under investigation was found to be twinned by rotational and inversion merohedry. In the higher symmetry setting, the trinuclear complex would feature exact inversion symmetry, and the two binuclear cationic complexes would be inversion counterparts of each other. The R3¯ symmetry is broken by a mismatch of less than 1Å between one pair of ligands L between the dinuclear cations, which feature slightly different rotational angles around the Cd ion in the otherwise symmetry equivalent complexes. This compound is also investigated by FT-IR and solid-state 13CCP-MAS NMR spectroscopies.

Poly[[tri-μ-aqua-do-deca-aqua-tris-(μ3-1-hy-droxy-ethyl-idene-1,1-di-phospho-nato)tricalcium(II)tripalladium(II)] penta-hydrate

The asymmetric unit of the title compound, {[CaPd{CH3OHC(PO3)2}(H2O)5]·5/3H2O}n, consists of one half of the complex [Pd{CH3OHC(PO3)2}]2− anion (point group symmetry m..), one Ca2+ cation [site symmetry (.2.)] that is surrounded by three water mol­ecules (one of which is on the same rotation axis) and by three disordered lattice water mol­ecules. The anions form a trinuclear metallocycle around a crystallographic threefold rotation axis. The cations are related by a twofold rotation axis to form a [Ca2(H2O)10]2+ dimer. The slightly distorted square-planar coordination environment of the PdII atoms in the complex anions is formed by O atoms of the bidentate chelating phospho­nate groups of the 1-hy­droxy­ethyl­idene-1,1-di­phospho­nate ligands. In the crystal, cations are bound to anions through —Ca—O—P—O— bonds, as well as through O—H⋯O hydrogen bonds, resulting in a three-dimensional polymer. The structure is completed by five disordered solvent mol­ecules localized in cavities within the framework.

Copper scandium zirconium phosphate: occupancy of theM1 andM2 sites in the temperature range 100–300 K

The title compound, with nominal formula Cu(2)ScZr(PO(4))(3), has a beige coloration and displays fast Cu(+) cation conduction at elevated temperatures. It adopts a NASICON-type structure in the space group R3c. The examined crystal was an obverse-reverse twin with approximately equal twin components. The [Sc(III)Zr(IV)(PO(4))(3)](2-) framework is composed of corner-sharing Sc/ZrO(6) octahedra and PO(4) tetrahedra. The Sc and Zr atoms are disordered on one atomic site on a crystallographic threefold axis. The P atom of the phosphate group lies on a crystallographic twofold axis. Nonframework Cu(+) cations occupy three positions. Two of the Cu(+) positions generate an approximately circular distribution around a site of 3 symmetry, referred to as the M1 site in the NASICON-type structure. The other Cu(+) position is situated close to the twofold symmetric M2 site, displaced into a position with a distorted square-based pyramidal coordination geometry. The structure has been determined at 100, 200 and 300 K. Changes in the refined site-occupancy factors of the Cu(+) positions suggest increased mobility of Cu(+) around the circular orbit close to the M1 site at room temperature, but no movement into or out of the M2 site. Free refinement of the Cu site-occupancy factors suggests that the formula of the crystal is Cu(1.92(1))ScZr(PO(4))(3), which is consistent with the low-level presence of Cu(2+) exclusively in the M2 site.

A Genuine Two‐Dimensional Ising Ferromagnet with Magnetically Driven Re‐entrant Transition

BaFe2(PO4)2 consists of honeycomb layers containing high-spin d6 Fe2+ ions. It is the first genuine two-dimensional oxide Ising ferromagnet (FM) with uniaxial magnetism parallel to the crystallographic three-fold axis. BaFe2(PO4)2 undergoes a re-entrant structural transition between 170 K and its FM critical temperature (65.5 K) owing to competition between the uniaxial magnetism and Jahn–Teller instability.

Tris{2-[(2,6-dimethylphenyl)amino]ethyl}amine

The title compound, C30H42N4, is an aryl­ated tris­(amino­eth­yl)amine derivative which was obtained by reducing the corresponding tris-amide with AlH3. The asymmetric unit consists of one third of a C 3v-symmetric mol­ecule with the tertiary N atom lying on a crystallographic threefold axis.

Two new transition metal inorganic–organic hybrid borates: [tris(2-aminoethoxy)trihydroxyhexaborato]cobalt(II) and its nickel(II) analogue

The two isomorphous title compounds, [1,5,9-tris(2-aminoethoxy)-3,7,11-trihydroxy-3,7,11-tribora-1,5,9-triborata-2,4,6,8,10,12-hexaoxa-13-oxoniatricyclo[7.3.1.0(5,13)]tridecane]cobalt(II), [Co(C(6)H(21)B(6)N(3)O(13))] or Co{B(6)O(7)(OH)(3)[O(CH(2))(2)NH(2)](3)}, and the Ni(II) analogue, [Ni(C(6)H(21)B(6)N(3)O(13))], each consist of an M(II) cation and an inorganic-organic hybrid {B(6)O(7)(OH)(3)[O(CH(2))(2)NH(2)](3)}(2-) anion. The M(II) cation lies on a crystallographic threefold axis (as does one O atom) and is octahedrally coordinated by three N atoms from the organic component. Three O atoms covalently link the B-O cluster and the organic component. Molecules are connected to one another through N-H···O and O-H···O hydrogen bonds, forming a three-dimensional supramolecular network.

Tris(6-carboxypyridine-2-carboxylato)terbium(III) 2.75-hydrate

In the title compound, [Tb(C7H4NO4)3]·2.75H2O, the Tb3+ atom is coordinated by three tridentate 6-carb­oxy­pyridine-2-carboxyl­ate ligands and lies on a crystallographic threefold rotation axis. The coordination polyhedron around TbIII adopts a distorted tricapped trigonal–prismatic geometry. Disordered water mol­ecules with partial occupancy are also present in the crystal, one of which is associated with each of the carboxyl­ate O atoms of the complex unit.

Tris{2-[(2-aminobenzylidene)amino]ethyl}amine

The title Schiff base, C27H33N7, is a tripodal amine displaying C 3 symmetry, with the central tertiary N atom lying on the threefold crystallographic axis. The N—CH2—CH2—N conformation of the pendant arms is gauche [torsion angle = 76.1 (3)°], which results in a claw-like mol­ecule, with the terminal aniline groups wrapped around the symmetry axis. The lone pair of the apical N atom is clearly oriented inwards towards the cavity, and should thus be chemically inactive. The amine NH2 substituents lie in the plane of the benzene ring to which they are bonded. With such an arrangement, one amine H atom forms an S(6) motif through a weak N—H⋯N hydrogen bond with the imine N atom, while the other is engaged in an inter­molecular N—H⋯π contact involving the benzene ring of a neighbouring mol­ecule related by inversion. The benzene rings also participate in an intra­molecular C—H⋯π contact of similar strength. In the crystal structure, mol­ecules are separated by empty voids (ca 5% of the crystal volume), although the crystal seems to be unsolvated.

ChemInform Abstract: The Structure of Triphenylmethanol, Ph3COH.

C19H160 , Mr = 260.3, trigonal, R3, a = 19.307 (3), c = 26.735 (4) A, V= 8631 (2) A 3, Z= 24, Dx = 1.20 g cm -3, a(Mo Ka) = 0.71073/~, /.~ = 0.7 cm -1, F(000) = 3312, T = 294 K, R = 0.083, wR = 0.068 for 1022 observed reflections. The structure contains hydrogen-bonded pyramidal tetramers (which have approximate 32 symmetry) with one molecule lying on a crystallographic threefold axis and another in a general position. The analysis was complicated by disorder in the crystal lattice where 71% of the tetramers occupy one orientation and 29% another; these moieties have their phenyl rings in the same volume elements in the lattice. The O...O separations in the hydrogen-bond systems are 2.884 (10) and 2.896 (11)/~ in the major tetramer and 2.80 (3) and 2.90 (3) A in the minor tetramer. Introduction. We have been interested for some time in the structures of the series Ph3MOH (M = C, Si, Ge, Sn, Pb). Although full structural data are avail- able (see below) for the Si, Ge, Sn and Pb derivatives, no structural data are available for the Ph3COH

Structures of two truncated phage-tail hyaluronate lyases from Streptococcus pyogenes serotype M1.

The crystal structures of truncated forms of the Streptococcus pyogenes phage-encoded hyaluronate lyases HylP2 and HylP3 were determined by molecular replacement to 1.6 and 1.9 A resolution, respectively. The truncated forms crystallized in a hexagonal space group, forming a trimer around the threefold crystallographic axis. The arrangement of the fold is very similar to that observed in the structure of the related hyaluronate lyase HylP1. The structural elements putatively involved in substrate recognition are found to be conserved in both the HylP2 and HylP3 fragments.

Tris(3,5-diphenylpyrazolyl)hydroborato]nickel(II) bromide

In the title tris­(pyrazol­yl)borate (TpPh2) complex, [NiBr(C45H34BN6)], the Ni, Br and B atoms lie on a crystallographic threefold axis and a distorted NiN3Br tetra­hedral geometry arises for the metal ion. In the crystal, C—H⋯(C=C) and C—H⋯π inter­actions help to establish the polar crystal packing.

The neutral cluster amminehexa-μ2-chlorido-μ4-oxido-tris(1,4,6-triazabicyclo[3.3.0]oct-4-ene)tetracopper(II)

The title compound, [Cu(4)Cl(6)O(C(5)H(9)N(3))(3)(NH(3))], is a neutral conformationally chiral cluster which crystallizes under the conditions described in this paper as a racemic conglomerate. It contains four Cu(II) atoms in a tetrahedral coordination with a central O atom lying on a crystallographic threefold axis. Six chloride anions bridge the four Cu(II) atoms. Three Cu(II) atoms are bound by an N atom of a monodentate 1,4,6-triazabicyclo[3.3.0]oct-4-ene (Htbo) ligand and the remaining Cu(II) atom is bound by a terminal ammine ligand. The geometry at each copper center is trigonal bipyramidal, produced by the bound N atom of Htbo or ammonia, the O atom in the axial position, and three chloride ions in the equatorial plane. The chloride anions form an octahedron about the oxygen center. The copper-ammonia bond lies along the crystallographic threefold axis, along which the molecules are packed in a polar head-to-tail fashion.

Violation of axial symmetry of optical properties in the trigonal crystal Nd:GdFe 2.1Ga 0.9(BO 3) 4

Strong dependence of birefringence and absorption spectra of d– d, f– f and charge transfer transitions on the direction of light beam in the plane perpendicular to the threefold crystallographic axis has been found out in trigonal crystal Nd:GdFe 2.1Ga 0.9(BO 3) 4. X-ray measurements have shown that the crystal consists of inversion twins, whose formation is stimulated by the partial substitution of Fe by Ga. Observed violation of axial symmetry of the trigonal crystal optical properties is accounted for on the basis of assumption about stripe domain structure of the inversion twins.

Syntheses and crystal structures of (2.2.2-cryptand)potassium chloride and (2.2.2-cryptand)ammonium bromide(0.75)chloride(0.25) hydrates

Two new complexes were synthesized, namely, 7: 2 (2.2.2-cryptand)potassium chloride and (2.2.2-cryptand)ammonium bromide(0.75)chloride(0.25) hydrates: [M(Crypt-222)]+ · Hal− · 3.5H2O, where M = K, Hal = Cl (I) and M = NH4, Hal = Br0.75Cl0.25 (II). The structures of two isomorphous crystals were studied by X-ray diffraction analysis. Trigonal (space group P\( \bar 3 \), Z = 2) structures I (a = 11.763 A, c = 11.262 A) and II (a = 11.945 A, c = 11.337 A) were solved by direct methods and refined by the full-matrix least-squares method in the anisotropic approximation to R = 0.057 (I) and 0.065 (II) for all 2626 (I) and 1654 (II) independent measured reflections (CAD-4 automated diffractometer, λMoKα). In structures I and II, the host-guest [M(Crypt-222)]+ complex cation lies on the threefold crystallographic axis and has the approximate D3 symmetry. In complex I, the coordination polyhedron of the K+ cation (CN = 8) is a bicapped trigonal prism somewhat distorted toward an antiprism. Complexes I and II contain H-bonded disordered cubes of the water molecules and the Cl− or Br− anions.