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: The higher resolution structural information on the active site of inositol monophosphatase will facilitate the design of substrate-based inhibitors and aid in the development of better therapeutic agents for bipolar disorder (manic depression).
Abstract: Inositol monophosphatase is a key enzyme of the phosphatidylinositol signalling pathway and the putative target of the mood-stabilizing drug lithium. The crystal structure of bovine inositol monophosphatase has been determined at 1.4 A resolution in complex with the physiological magnesium ion ligands. Three magnesium ions are octahedrally coordinated at the active site of each of the two subunits of the inositol monophosphatase dimer and a detailed three-metal mechanism is proposed. Ligands to the three metals include the side chains of Glu70, Asp90, Asp93 and Asp220, the backbone carbonyl group of Ile92 and several solvent molecules, including the proposed nucleophilic water molecule (W1) ligated by both Mg-1 and Mg-3. Modelling of the phosphate moiety of inositol monophosphate to superpose the axial phosphate O atoms onto three active-site water molecules orientates the phosphoester bond for in-line attack by the nucleophilic water which is activated by Thr95. Modelling of the pentacoordinate transition state suggests that the 6-OH group of the inositol moiety stabilizes the developing negative charge by hydrogen bonding to a phosphate O atom. Modelling of the post-reaction complex suggests a role for a second water molecule (W2) ligated by Mg-2 and Asp220 in protonating the departing inositolate. This second water molecule is absent in related structures in which lithium is bound at site 2, providing a rationale for enzyme inhibition by this simple monovalent cation. The higher resolution structural information on the active site of inositol monophosphatase will facilitate the design of substrate-based inhibitors and aid in the development of better therapeutic agents for bipolar disorder (manic depression).
57 citations
TL;DR: The evidence for the effectiveness of ascorbate as a radioprotectant was strengthened, and quinone, 2,2,6,6-tetramethyl-4-piperidone, and reduced dithiothreitol showed promise as radiop rotatedectants.
Abstract: Radiation damage continues to present a problem to crystallographers using cryocooled protein crystals at third-generation synchrotrons. Free-radical scavengers have been suggested as a possible means of reducing the rate of this damage. The screening of a large number of potential radioprotectants was undertaken with an online microspectrophotometer using cystine and cysteine to model protein disulfide bonds and thiol groups, respectively. Oxidized α-lipoic acid was tested as a possible model disulfide bond. The evidence for the effectiveness of ascorbate as a radioprotectant was strengthened, and quinone, 2,2,6,6-tetramethyl-4-piperidone, and reduced dithiothreitol showed promise as radioprotectants.
57 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Macromolecular crystals are routinely flash-cooled to, and held at, 100 K during most X-ray diffraction experiments in order to suppress secondary radiation damage caused by thermally mobile radicals (Hope, 1988; Garman & Schneider, 1997; Rodgers, 1997; Garman, 1999)....
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...Keywords: radioprotectants; radiation damage; macromolecular cryocrystallography....
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TL;DR: The structure of the non-glycosyl-ated recombinant enzyme has been determined by molecular replacement and refined against 1.7 A resolution synchrotron data to an R factor of 14.6% and is the first report of the three-dimensional structure of a yeast family 15 glucoamylase.
Abstract: The yeast Saccharomycopsis fibuligera produces a glucoamylase which belongs to sequence family 15 of glycosyl hydrolases. The structure of the non-glycosylated recombinant enzyme has been determined by molecular replacement and refined against 1.7 A resolution synchrotron data to an R factor of 14.6%. This is the first report of the three-dimensional structure of a yeast family 15 glucoamylase. The refinement from the initial molecular-replacement model was not straightforward. It involved the use of an unrestrained automated refinement procedure (uARP) in combination with the maximum-likelihood refinement program REFMAC. The enzyme consists of 492 amino-acid residues and has 14 α-helices, 12 of which form an (α/α)6 barrel. It contains a single catalytic domain but no starch-binding domain. The fold of the molecule and the active site are compared to the known structure of the catalytic domain of a fungal family 15 glucoamylase and are shown to be closely similar. The active- and specificity-site residues are especially highly conserved. The model of the acarbose inhibitor from the analysis of the fungal enzyme fits tightly into the present structure. The active-site topology is a pocket and hydrolysis proceeds with inversion of the configuration at the anomeric carbon. The enzyme acts as an exo-glycosyl hydrolase. There is a Tris [2-amino-2-(hydroxymethyl)-1,3-propanediol] molecule acting as an inhibitor in the active-site pocket.
57 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...(a) and (b) Orthogonal stereo ribbon representations of GluSf plotted by MOLSCRIPT (Kraulis, 1991)....
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TL;DR: Three-dimensional electron diffraction methods for phase identification and structure determination of polycrystalline powder materials and the determination of very complex structures from nano- and micron-sized crystals.
57 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...These include direct methods [e.g. the programs SHELX (Sheldrick, 2008) and SIR (Altomare et al., 1999, 2008)], 272 Yifeng Yun et al. Three-dimensional electron diffraction IUCrJ (2015)....
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...2, 267–282 charge flipping [e.g. the programs SUPERFLIP (Palatinus & Chapuis, 2007) and JANA (Petřı́ček et al., 2014)] and simulated annealing (e.g. SIR)....
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...The most common technique for structure determination of crystalline materials is SCXRD, which can only be used for crystals larger than 10 mm with in-house diffractometers or a few microns with synchrotron light sources....
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...Different methods have been developed to facilitate structure solution using powder diffraction data, for example direct methods (Altomare et al., 1999, 2008) and charge-flipping (Baerlocher, McCusker & Palatinus, 2007)....
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TL;DR: A review is given of the mathematical procedures required for a molecular-replacement structure determination and of the situations where a known homologous structure can be used as a search model and to phase determination in the presence of non-crystallographic symmetry.
Abstract: A review is given of the mathematical procedures required for a molecular-replacement structure determination. These apply equally to the more frequently encountered situations where a known homologous structure can be used as a search model and to phase determination in the presence of non-crystallographic symmetry (NCS). In general, the former represents improper NCS between two different unit cells, whereas the latter occurs when there is proper NCS within one unit cell.
57 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...The superimposed Pattersons are then integrated over the volume U....
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...Foremost among these programs are AMoRe by Navaza (1994), DM (Cowtan, 1994), CNS (Brunger et al., 1998) and Patsol (Tong, 1993)....
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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