J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: X-ray crystallography and small angle x-ray scattering are combined to elucidate the structure of the central region of the plakin domain of plectin, which corresponds to the SR3, SR4, SR5, and SH3 domains.
46 citations
TL;DR: Comparison of the structure of acid-beta-glucosidase with that of xylanase, a bacterial enzyme from a closely related protein family, demonstrates a close correspondence between the active-site residues of the two enzymes.
Abstract: Gaucher disease is caused by mutations in the gene encoding acid-β-glucosidase. A recombinant form of this enzyme, Cerezyme®, is used to treat Gaucher disease patients by `enzyme-replacement therapy'. Crystals of Cerezyme® after its partial deglycosylation were obtained earlier and the structure was solved to 2.0 A resolution [Dvir et al. (2003), EMBO Rep. 4, 704–709]. The crystal structure of unmodified Cerezyme® is now reported, in which a substantial number of sugar residues bound to three asparagines via N-glycosylation could be visualized. The structure of intact fully glycosylated Cerezyme® is virtually identical to that of the partially deglycosylated enzyme. However, the three loops at the entrance to the active site, which were previously observed in alternative conformations, display additional variability in their structures. Comparison of the structure of acid-β-glucosidase with that of xylanase, a bacterial enzyme from a closely related protein family, demonstrates a close correspondence between the active-site residues of the two enzymes.
46 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Crystals were mounted and flash-cooled at 100 K. X-ray diffraction images were processed using XDS and XSCALE (Kabsch, 1993)....
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...Residues 312–319 (loop 3) in molecule B of the GCase model did not fit the electron density....
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TL;DR: A graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation, which locates examples of similar base rearrangements that are important in structural regulation.
Abstract: We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.
46 citations
TL;DR: A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM), and geometric singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states.
Abstract: A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM). This approach is compared to all-atom computer simulations. The simulations reveal complex hydration effects within the (concave) receptor pocket, sensitive to the distance of the (convex) approaching ligand. The ligand induces and controls an intermittent switching between dry and wet states of the hosting pocket, which determines the range and magnitude of the pocket-ligand attraction. In the level-set VISM, a geometric free-energy functional of all possible solute-solvent interfaces coupled to the local dispersion potential is minimized numerically. This approach captures the distinct metastable states that correspond to topologically different solute-solvent interfaces, and thereby reproduces the bimodal hydration behavior observed in the all-atom simulation. Geometrical singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states. While the hydration phenomena can thus be explained by capillary effects, the explicit inclusion of dispersion and curvature corrections seems to be essential for a quantitative description of hydrophobically confined systems on nanoscales. This study may shed more light onto the tight connection between geometric and energetic aspects of biomolecular hydration and may represent a valuable step toward the proper interpretation of experimental receptor-ligand binding rates.
46 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...…receptor plays a key role in biomolecular assembly processes, such as proteinligand recognition [7–12], the binding of the human immunodeficiency virus (HIV) [13] or the dengue virus [14] to human cells, the inhibition of influenza virus infectivity [15], or in synthetic host-guest systems [16]....
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TL;DR: In this article, solid-solution studies in the CsHSO 4 -CsH 2 PO 4 system carried out in a search for low-temperature proton conducting materials yielded the new compound Cs 3 (HSO4 )2(H 2PO 4 ) [tricesium bis(hydrogensulfate) dihydrogenphosphate], which is a rhombohedral, pseudo-body-centered cubic, with lattice constants a = 6.95 (2) A and α ≃ 90°.
Abstract: Solid-solution studies in the CsHSO 4 -CsH 2 PO 4 system carried out in a search for low-temperature proton conducting materials yielded the new compound Cs 3 (HSO 4 )2(H 2 PO 4 ) [tricesium bis(hydrogensulfate) dihydrogenphosphate]. Single-crystal X-ray measurements (performed at room temperature) revealed that Cs 3 (HSO 4 )2(H 2 PO 4 ) crystallizes in space group P2 1 /n and has lattice parameters a = 19.546(3), b = 7.8798(10), c = 9.1854(17)A and β = 100.536(14)°. With four formula units in the unit cell, and a cell volume of 1390.7(4)A 3 , Cs 3 (HSO 4 )2(H 2 PO 4 ) has a calculated density of 3.295Mg m -3 . 18 non-H atoms were located in the asymmetric unit. Refinement using anisotropic temperature factors for all 18 non-H atoms yielded weighted residuals based on F 2 and F values, respectively, of 9.32 and 4.56% for all observed reflections. Hydrogen sites were identified (but not refined) on the basis of geometric considerations. The structure contains zigzag chains of hydrogen-bonded anion tetrahedra that are, in turn, bonded to one another to form a three-dimensional structure. In the temperature range 381-398K the compound transforms into a structure which is rhombohedral, pseudo-body-centered cubic, with lattice constants a = 6.95 (2) A and α ≃ 90°.
46 citations
References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
18,531 citations
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations