102,673 research outputs found
<i>ShelXle</i>: a Qt graphical user interface for<i>SHELXL</i>
No full textShelXleis a graphical user interface forSHELXL[Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for theSHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features ofShelXleinclude intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions.ShelXleis completely compatible with all features ofSHELXLand is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.</jats:p
The Antiviral Antibiotic Feglymycin First Direct Methods Solution of a 1000Plus Equal Atom Structure
No full textThe double helical structure adopted by the antiviral peptide feglymycin see picture is reminiscent of that of gramicidin, but feglymycin is more likely to function as an ion carrier than as a membrane channel. With more than 1000 unique atoms this is the largest equal atom crystal structure solved by ab initio direct method
Structure of the lipopeptide antibiotic tsushimycin
No full textThe amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 angstrom resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding
Structure of the C2A domain of rabphilin-3A.
No full textRabphilin-3A is a neuronal protein containing a C2-domain tandem. To date, only the structure of the C2B domain has been solved. The crystal structure of the Ca2+-free C2A domain has been solved by molecular replacement and refined to 1.92 angstrom resolution. It adopts the classical C2-domain fold consisting of an eight-stranded antiparallel beta-sandwich with type I topology. In agreement with its Ca2+-dependent negatively charged membrane-binding properties, this C2 domain contains all the conserved acidic residues responsible for calcium binding. However, the replacement of a conserved aspartic acid residue by glutamic acid allows formation of an additional strong hydrogen bond, resulting in increased rigidity of calcium-binding loop 1. The electrostatic surface of the C2A domain consists of a large positively charged belt surrounded by two negatively charged patches located at both tips of the domain. In comparison, the structurally very similar C2A domain of synaptotagmin I has a highly acidic electrostatic surface, suggesting completely unrelated functions for these two C2A domains
The molecular structure and crystal organization of rac-terfenadine/beta-cyclodextrin/tartaric acid multicomponent inclusion complex
No full textThe crystalline ternary inclusion complex terfenadine/beta-cyclodextrin/tartaric acid (TFN/betaCD/TA, 2:4:1) has been prepared from a aqueous solution (terfenadine, TFN, rac-alpha-[4-(1,1-dimethylethyl)phenyl]-4-(hydroxydiphenylmethyl)-1-piperidine-butanol). The solubility of the multicomponent system in water is remarkably different from that of the single components. The crystal structure shows that the TFN guest adopts an extended conformation and that the diphenyl end of the molecule is docked in the cavity formed by the association of two independent betaCD molecules through hydrogen bonds connecting their wide rims. The structure of the dimer is deformed with respect to uncomplexed betaCDs, due to the shape of the guest. The two aromatic rings interact differently with the macrocycles forming the dimer, one being included perpendicular in the central cavity of one betaCD, the other laying parallel to the interface between the two rims. The t-Bu- end of the guest is included in the cavity of a betaCD belonging to a different dimer, entering from the side of the narrow rim. The central part of the guest is surrounded by water molecules and tartaric acid, which creates a hydrophilic microenvironment in the interstices among dimers. The enhanced solubility of the multicomponent system could be related to the hydrogen bonds between the tartaric acid and the oxygens belonging to the wide rims. The overall structural arrangement of the betaCD units is driven by the shape of the TFN guest which needs a hydrophobic environment at both ends. The lipophilic interactions between TFN and betaCD cavities are responsible for the relevant perturbation in the regularity of the packing of the hosts
The coordination chemistry of functionalised poly(pyrazol-1-yl)borate ligands and the photophysical properties of cyanide-bridged d-f hybrids
No full textThe content of this thesis is concerned with two distinctly independent areas of
research: (i) the synthesis and study of new poly(pyrazol-1-yl)borate ligands and
their metal complexes; (ii) crystallographic and photophysical studies of new d-f
hybrid complexes.
Chapter One is divided into three parts: Part one gives a general introduction
to poly(pyrazol-1-yl)borate chemistry along with a concise and up-to-date review of
those ligands containing substituents in the C3 position of the pyrazolyl ring; part two
provides a brief introduction into the physical properties of lanthanide(III) metal
ions, as well as describing the practical applications of their individual spectroscopic
properties; and part three contains a brief review on the structural chemistry of
cyanide-bridged coordination polymers.
Chapter Two describes the syntheses of four new scorpionates: dihydrobis[3-(4-pyridyl)pyrazol-1-yl]borate (Bp4py); dihydro-bis[3-(3-pyridyl)pyrazol-1-
yl]borate (Bp3py); hydro-tris[3-(4-pyridyl)pyrazol-1-yl]borate (Tp4py) and hydrotris[3-(3-pyridyl)pyrazol-1-yl]borate (Tp3py). A series of X-ray crystallographic
studies reveals a range of mononuclear, dinuclear and polymeric coordination
complexes with various metal ions.
Chapter Three describes a range of structural and photophysical studies on
lanthanide(III) complexes of poly(pyrazol-1-yl)borate ligands. New mixed-ligand
lanthanide(III) complexes with various combinations of the anionic ligands Tp2py
,
Bp2py and dibenzoylmethane (dbm) were prepared and structurally characterised.
Photophysical studies on the isostructual series [Ln(Bp2py)(dbm)2] (Ln = Pr, Nd, Er,
Yb) show characteristic near-IR luminescence from the lanthanide ion. Near-IR
luminescence was also demonstrated from the complexes [Ln(Bp2py)
2(NO3)] and
[Ln(Tp2py)(NO3)
2] (Ln = Pr, Er), upon suitable excitation of the ligand
chromophores.
Chapter Four describes the structural and photophysical properties of new
cyanide-bridged d-f coordination polymers. Structural and photophysical studies are
presented for a series of Ru-Ln complexes based on the [Ru(bipy)(CN)4]
2- donor unit
connected to a Ln(III) energy-acceptor via cyanide bridges (where bipy is 2,2’-
bipyridine and Ln = Pr, Nd, Er, Yb). Structural and photophysical studies were also
performed on [Cr(CN)6][Ln(DMF)4(H2
O)2] complexes, in which the lanthanide ion
(Ln = Nd, Yb) acts as the energy acceptor from the hexacyanochromate
chromophore. The structures of [Cr(CN)6][Ln(H2
O)2] (Ln = Gd, Yb) and
K2[Ru(phen)(CN)4] (where phen = 1,10-phenanthroline) are also presented.
Chapter Five gives a brief review of the field of X-Ray Crystallography with
analysis of the history and theory of the technique, as well as an overview of its
practical aspects used in this work. A few crystal structures solved by the author,
and independent of the topics in this thesis, are also reported
In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case
No full textSAD (single-wavelength anomalous diffraction) has enormous potential for phasing proteins using only the anomalous signal of the almost ubiquitous native sulfur, but requires extremely precise data. The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 Angstrom using a CCD detector with a rotating-anode generator and three-circle goniometer. The seven 'super-S' atoms (disulfide bridges) were located by dual-space recycling with SHELXD and the high solvent content enabled the density-modification program SHELXE to generate high-quality maps despite the modest resolution. Subsequently, a 2.05 Angstrom synchrotron data set was collected and used for further phase extension and structure refinement
Structures of glycopeptide antibiotics with peptides that model bacterial cell-wall precursors
No full textThe vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (< 1 Angstrom). In addition to the features expected from previous structural and spectroscopic studies, two new motifs were observed that may prove important in the design of antibiotics modified to overcome bacterial resistance. A changed binding mode was found in two dipeptide complexes, and a new type of face-to-face oligomerization (in addition to the well-established back-to-back dimerization) was seen when the model peptide reaches a critical fraction of the size of the cell-wall precursor pentapeptide. The extensive interactions involving both antibiotic and peptide molecules in this interface should appreciably enhance the kinetic and thermodynamic stability of the complexes. In the pentapeptide complex, the relative positions of the peptides are close to those required for D-Ala elimination, so this structure may provide a realistic model for the prevention of the enzyme-catalyzed cell-wall crosslinking by antibiotic binding. (C) 2002 Elsevier Science Ltd. All rights reserved
Crystal structures of cephaibols
No full textThe crystal structures of the peptaibol antibiotics cephaibol A, cephaibol B and cephaibol C have been determined at ca. 0.9 Angstrom resolution. All three adopt a helical conformation With a sharp bend (of about 55degrees) at the central hydroxyproline. All isovalines were found to possess the D configuration, superposition of all four models (there are two independent molecules in the cephaibol B structure) shows that the N-terminal helix is rigid and the C-terminus is flexible. There are differences in the hydrogen bonding patterns for the three structures that crystallize in different space groups despite relatively similar unit cell dimensions, but only in the case of cephaibol C does the packing emulate the formation of a membrane channel believed to be important for their biological function. Copyright (C) 2003 European Peptide Society and John Wiley Sons. Ltd
Improving radiation-damage substructures for RIP
No full textSpecific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing ( RIP) method. The method has been investigated for six disulfide-containing test structures ( elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57 sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage
- …
