scholarly journals Tris(Para-Tolyl)Bismuth Bis(Bromodifluoroacetate). Synthesis and Structure Features

2020 ◽  
Vol 12 (4) ◽  
pp. 72-78
Author(s):  
V. Senchurin ◽  
Keyword(s):  
Structural Data ◽  
Data Bank ◽  
Bismuth Atom ◽  
Cell Parameters ◽  
Bond Lengths ◽  
Tert Butyl Hydroperoxide ◽  
Graphite Monochromator ◽  
Intermolecular Contacts ◽  
Residual Electron Density ◽  
Distorted Trigonal Bipyramidal Coordination

The interaction of tri(para-tolyl)bismuth with tert-butyl hydroperoxide and bromodifluoroacetic acid in diethyl ether have synthesized tris(para-tolyl)bismuth bis(bromodifluoroacetate). The X-ray diffraction pattern for the crystal has been obtained at 293 K on an automatic diffractometer D8 Quest Bruker (MoKα-radiation, λ = 0.71073 Å, graphite monochromator), the results are [C25H21O4F4Br2Bi, M 830.22, the triclinic syngony, the symmetry group P–1; cell parameters: a = 10.292(8), b = 11.752(9), c = 12.693(9) Å, α = 89.42(2) degrees, β = 78.04(3) degrees, γ = 78.04(3) degrees; V = 1424.8(18) Å3; the crystal size is 0.73×0.57×0.41 mm; intervals of reflection indexes are –13 ≤ h ≤ 13, –15 ≤ k ≤ 15, –16 ≤ l ≤ 16; total reflections 45443; independent reflections 7096; Rint 0.1030; GOOF 1.049; R1 = 0.0739, wR2 = 0.1834; residual electron density 2.11/–2.78 e/Å3], the bismuth atom have a distorted trigonal-bipyramidal coordination. The OBiO axial angle is 172.2(3) degrees; the sum of the CBiC angles in the equatorial plane is 360.6. The Bi–O and Bi–C bond lengths are 2.275(8), 2.295(8) Å and 2.187(10)–2.212(13) Å. The Bi•••O=С distances are 3.127(10) and 3.159(10) Å, which is less than the sum of the van der Waals radii of bismuth and oxygen (3.59 Å). There are no intermolecular contacts H∙∙∙Hal in the crystal. Complete tables of coordinates of atoms, bond lengths and valence angles for the structure are deposited at the Cambridge Structural Data Bank (no. 1923097; [email protected]; http: //www.ccdc.cam.ac.uk).

scholarly journals Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

2020 ◽  
Vol 21 (4) ◽  
pp. 1352 ◽  
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
József Tőzsér
Keyword(s):  
Structural Characteristics ◽  
Limited Proteolysis ◽  
Structural Data ◽  
Data Bank ◽  
Life Cycles ◽  
Evolutionary Relationships ◽  
Multiple Sequence ◽  
Dimer Interface ◽  
Viral Proteases ◽  
Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

Compressibility of β-As4S4: an in situ high-pressure single-crystal X-ray study

2012 ◽  
Vol 76 (4) ◽  
pp. 963-973 ◽  
Author(s):  
G. O. Lepore ◽  
T. Boffa Ballaran ◽  
F. Nestola ◽  
L. Bindi ◽  
D. Pasqual ◽  
...  
Keyword(s):  
Pressure Range ◽  
Substantial Reduction ◽  
Structural Data ◽  
Unit Cell ◽  
Van Der Waals Interactions ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Intermolecular Distances

AbstractAmbient temperature X-ray diffraction data were collected at different pressures from two crystals of β-As4S4, which were made by heating realgar under vacuum at 295ºC for 24 h. These data were used to calculate the unit-cell parameters at pressures up to 6.86 GPa. Above 2.86 GPa, it was only possible to make an approximate measurement of the unit-cell parameters. As expected for a crystal structure that contains molecular units held together by weak van der Waals interactions, β-As4S4 has an exceptionally high compressibility. The compressibility data were fitted to a third-order Birch–Murnaghan equation of state with a resulting volume V0 = 808.2(2) Å3, bulk modulus K0 = 10.9(2) GPa and K' = 8.9(3). These values are extremely close to those reported for the low-temperature polymorph of As4S4, realgar, which contains the same As4S4 cage-molecule. Structural analysis showed that the unit-cell contraction is due mainly to the reduction in intermolecular distances, which causes a substantial reduction in the unit-cell volume (∼21% at 6.86 GPa). The cage-like As4S4 molecules are only slightly affected. No phase transitions occur in the pressure range investigated.Micro-Raman spectra, collected across the entire pressure range, show that the peaks associated with As–As stretching have the greatest pressure dependence; the S–As–S bending frequency and the As–S stretching have a much weaker dependence or no variation at all as the pressure increases; this is in excellent agreement with the structural data.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of a hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) fromCoffea canephorainvolved in chlorogenic acid biosynthesis

2012 ◽  
Vol 68 (7) ◽  
pp. 824-828 ◽  
Author(s):  
Laura A. Lallemand ◽  
James G. McCarthy ◽  
Sean McSweeney ◽  
Andrew A. McCarthy
Keyword(s):  
Structural Data ◽  
Coffea Canephora ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Key Enzyme ◽  
Substrate Specifities ◽  
Drop Technique ◽  
Better Than

Chlorogenic acids (CGAs) are a group of soluble phenolic compounds that are produced by a variety of plants, includingCoffea canephora(robusta coffee). The last step in CGA biosynthesis is generally catalysed by a specific hydroxycinnamoyl-CoA quinate hydroxycinnamoyltransferase (HQT), but it can also be catalysed by the more widely distributed hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT). Here, the cloning and overexpression of HCT fromC. canephorainEscherichia colias well as its purification and crystallization are presented. Crystals were obtained by the sitting-drop technique at 293 K and X-ray diffraction data were collected on the microfocus beamline ID23-2 at the ESRF. The HCT crystals diffracted to better than 3.0 Å resolution, belonged to space groupP42212 with unit-cell parametersa=b= 116.1,c= 158.9 Å and contained two molecules in the asymmetric unit. The structure was solved by molecular replacement and is currently under refinement. Such structural data are needed to decipher the molecular basis of the substrate specifities of this key enzyme, which belongs to the large plant acyl-CoA-dependent BAHD acyltransferase superfamily.

Accuracy of the final model

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Data Bank ◽  
The Other ◽  
Protein Crystal ◽  
Major Error ◽  
Final Model ◽  
Bond Angles ◽  
Bond Lengths ◽  
R Factor ◽  
Insight Into

The result of all the work described in the previous chapters will be a set of coordinates and other data suitable for deposit in the Protein Data Bank. You or I may use these coordinates, and we need to have some insight into their accuracy and reliability. In the previous chapters, indicators have been described, which may suggest aspects of the data or interpretation procedures that might lead to problems. But as the determination of protein crystal structures becomes more routine, many of these indicators are omitted from publications. Fortunately, crystallographic procedures are self-checking to a large extent. It is rare for a major error of interpretation to lead right through to a published refined structure. A high Rfree factor is a warning, especially if coupled with departures from the requirements of correct bond lengths, angles, and acceptable dihedral angles. On the other hand, there will always be a desire to squeeze more results from the data. All interpretations are subject to error; nearly all protein crystals have regions that are less ordered, where accurate interpretation is less feasible; and the structure may be overrefined, using too many variables for the data. If the majority of the molecule is correctly interpreted, a reasonable R factor may be obtained even though some small regions are completely wrong. During refinement it is usual to restrain the bond lengths and bond angles to be near their theoretical values, as described in Chapter 12. The extent to which bond lengths and bond angles depart from these values is often quoted as an indicator of accuracy. These departures are, however, difficult to interpret because they depend on how tightly the restraints have been applied. The same applies to the restraint of certain coordinates to lie in a plane. This difficulty illustrates a general problem. Designers of refinement procedures are understandably anxious to improve their procedures to lead directly to a well-refined structure. Every aspect of structure that can be recognized as having a regularity could, in principle, be expressed as a restraint which enforces it during refinement.

Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

2015 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Data Bank ◽  
Complex Shape ◽  
Structural Data ◽  
Data Bank ◽  
Robot Kinematics ◽  
Motion Prediction ◽  
Serial Manipulators ◽  
Localized Structures ◽  
Motion Modes ◽  
Structural Compliance

On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

Further analysis of surface bond lengths measured for chemisorption on metal surfaces

1986 ◽  
Vol 64 (7) ◽  
pp. 1385-1389 ◽  
Author(s):  
K. A. R. Mitchell ◽  
S. A. Schlatter ◽  
R. N. S. Sodhi
Keyword(s):  
Structural Data ◽  
Bond Lengths ◽  
Alternative Approach ◽  
Length Data ◽  
Surface Metal ◽  
Solid Compounds ◽  
General Reliability ◽  
Predictive Approaches ◽  
Model Structures ◽  
Surface Bond

This paper compares bond lengths deduced from the methods of surface crystallography with predictions from the Pauling–Schomaker–Stevenson approach and from a new alternative approach suggested by recent work of Brown and Altermatt. Examples considered are specifically for X—M surface bond lengths where atoms X from groups 16 or 17 are adsorbed on well-defined surfaces of a metal M. The alternative approach introduced here is parametrised with reference to structural data from solid compounds of formula MX. The two predictive approaches considered, when used together, appear to be quite adequate for guiding choices of trial model structures to be included in surface crystallographic analyses with low-energy electron diffraction (LEED); also they seem reasonable for checking the general reliability (or otherwise) of surface bond length data. Two further features introduced by this work are (i) evidence that the Cl—Ag distance reported by LEED for Cl adsorbed on the Ag(100) surface is broadly consistent with the structure of solid AgCl; (ii) evidence for S adsorbed on the Fe(110) surface that these analyses can guide investigations of lateral relaxations of surface metal atoms. As more reliable structural data become available, extensions of these analyses should help to identify the finer details in X—M bond lengths which result from the special coordination arrangements occurring at surfaces.

scholarly journals Understanding Structural Features of Microbial Lipases–-An Overview

2008 ◽  
Vol 3 ◽  
pp. ACI.S551 ◽  
Author(s):  
John Geraldine Sandana Mala ◽  
Satoru Takeuchi
Keyword(s):  
Structural Analysis ◽  
Candida Rugosa ◽  
Structural Data ◽  
Data Bank ◽  
Candida Rugosa Lipase ◽  
Structural Features ◽  
X Ray Crystallography ◽  
Versatile Tool ◽  
Microbial Lipases

The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) returns only 93 hits (as of September 2007) and, the NCBI database ( http://www.ncbi.nlm.nih.gov ) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

Computerized geological mapping in the Grenville Province, Quebec

1970 ◽  
Vol 7 (6) ◽  
pp. 1357-1373 ◽  
Author(s):  
H. R. Wynne-Edwards ◽  
A. Nandi ◽  
M. M. Kehlenbeck ◽  
A. F. Laurin ◽  
K. N. M. Sharma ◽  
...  
Keyword(s):  
Processing System ◽  
Structural Data ◽  
Data Bank ◽  
Geological Mapping ◽  
Grenville Province ◽  
Geological Interpretation ◽  
Rock Types ◽  
Potential Map ◽  
Computer Based ◽  
Project Data

Since 1965, the Quebec Department of Natural Resources has conducted reconnaissance mapping in the Grenville Province, completing to date over 70 000 square miles (181 000 km2). In 1968 a computer-based data processing system was designed at Queen's University, and applied to this Grenville Project. Data are recorded in the field on input documents designed to recover a complete description of the structure and lithology of an outcrop in a standard and reproducible form. From these records a data bank, now with descriptions of over 5000 outcrops, has been constructed for the field seasons of 1968 and 1969. Lthological sorting programs based on the textural and mineralogical qualities used to define rock types have been written to provide listings of some 40 potential map-units. Outcrop maps identifying lithologies have been drawn on a computer-driven drum plotter to provide the geologist with a basic document from which to make geological interpretation. Structural data have been extracted and plotted in equal-area projections, and also plotted on maps directly by machine, using standard structural symbols for layering, foliation, and lineation. The system has upgraded the standard of data collection in the field, and provides a rapid and versatile means of handling data and of interpreting the geology. The data bank, when made publicly available, will enable users of government geological maps and reports to reinterpret the area in their own manner, or freely to add any proprietary data in the preparation of revisions.

The crystal and molecular structure of anti-1,2,4,5-tetraphenyl-3,6-dicarbomethoxytricyclo[3.1.0.02,4]hexane

1978 ◽  
Vol 56 (10) ◽  
pp. 1364-1367 ◽  
Author(s):  
M. J. Bennett ◽  
J. T. Purdham
Keyword(s):  
Molecular Structure ◽  
Least Squares ◽  
Experimental Error ◽  
Crystal And Molecular Structure ◽  
Structural Data ◽  
Monoclinic Space Group ◽  
Full Matrix ◽  
Bond Lengths ◽  
Highly Strained ◽  
Least Squares Techniques

1,2,4,5-Tetraphenyl-3,6-dicarbornethoxytricyclo[3.1.0.02,4]hexane crystallizes in the monoclinic space group P21/c with a = 10.044(4), b = 9.500(2), c = 14.172(4) Å, β = 104.38(2)°, and Z = 2. Using 1032 unique reflections with I > 3σ(I), the structural data were refined by full matrix least-squares techniques to R = 0.038. The molecule was found to be in the anti-configuration. All bond lengths within the highly strained central tricyclic framework were equal within experimental error and average 1.531 Å.

Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses

2016 ◽  
Vol 72 (3) ◽  
pp. 324-337 ◽  
Author(s):  
A. Janner
Keyword(s):  
Lattice Point ◽  
Three Dimensional ◽  
Structural Data ◽  
Data Bank ◽  
Coarse Grained ◽  
Large Set ◽  
Fine Grained ◽  
Coarse Grained Model ◽  
Digital Modeling ◽  
Icosahedral Viruses

Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article.

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