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 S-SAD approach relies on the anomalous signal of sulfur naturally occurring in proteins and alleviates all need for sample derivatization, and may be applicable to all protein crystals able to provide accurate diffraction data.
Abstract: Recent years have witnessed significant advancements in X-ray data-acquisition techniques and phasing algorithms, which have made possible the successful use of a very small anomalous diffraction signal for the solution of crystal structures of macromolecules. Two crystal structures, a 44 kDa glucose isomerase containing nine sulfurs and a 33 kDa xylanase containing five sulfurs, have been solved from single-wavelength anomalous data using widely available methods and programs. These two enzymes contain less sulfur than most proteins in the bacterial or eukaryotic proteomes, providing a Bijvoet ratio of about 0.6%. For glucose isomerase the automatically interpretable electron-density maps could be obtained at high as well as low resolution. The S-SAD approach relies on the anomalous signal of sulfur naturally occurring in proteins and alleviates all need for sample derivatization. It may therefore be applicable to all protein crystals able to provide accurate diffraction data.
53 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The K absorption edges of P, S and Cl lie in the longwavelength region of X-ray radiation, at 5.78, 5.02 and 4.39 AÊ , electronic reprint respectively, according to CROSSEC (Cromer, 1983)....
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...All diffraction data were collected on beamlines X9A and X9B at NSLS (Brookhaven National Laboratory) using Quantum4 ADSC CCD (X9B) or MAR CCD (X9A) detec- tors and were processed with HKL2000 (Otwinowski & Minor, 1997)....
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TL;DR: New copper(II) complexes—dimeric-[Cu(nphen)(gly)(H2O)]+ (1) and [Cu(dmphen)(gly) (NO3)(H 2O)] (2) (nphen = 5-nitro-1, 10-phenanthroline, dmphen = 4,7-dimethyl-1-10-phenAnthroline and gly = glycine)— have been tested for their in vitro DNA/
Abstract: New copper(II) complexes—dimeric-[Cu(nphen)(gly)(H2O)]+ (1) and [Cu(dmphen)(gly)(NO3)(H2O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline, and gly = glycine)—have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR, EPR spectroscopy, and cyclic voltammetry. The CT-DNA-binding properties of these complexes have been investigated by thermal denaturation measurements and both absorption and emission spectroscopy. The DNA cleavage activity of these complexes has been studied on supercoiled pUC19 plasmid DNA by gel electrophoresis experiments in the absence and presence of H2O2. Furthermore, the interaction of these complexes with bovine serum albumin (BSA) has been investigated using absorption and emission spectroscopy. The thermodynamic parameters, free-energy change (ΔG), enthalpy change (ΔH), and entropy change (ΔS) for BSA + complexes 1 and 2 systems have been calculated by the van’t Hoff equation at three different temperatures (293.2, 303.2, and 310.2 K). The distance between the BSA and these complexes has been determined using fluorescence resonance energy transfer (FRET). Conformational changes of BSA have been observed using the synchronous fluorescence technique. In addition, in vitro cytotoxicities of these complexes on tumor cell lines (Caco-2, A549, and MCF-7) and healthy cells (BEAS-2B) have been examined. The antimicrobial activity of the complexes has also been tested on certain bacteria cells. The effect of mono and dimeric in the above complexes is presented and discussed. New copper(II) complexes—dimeric-[Cu(nphen)(gly)(H2O)]+ (1) and [Cu(dmphen)(gly) (NO3)(H2O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline and gly = glycine)—have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR and EPR spectroscopy. They have been tested for their in vitro DNA/BSA interactions by the spectroscopic methods. These complexes exhibited higher cytotoxic and antimicrobial activities. Complex 1 shows better DNA / BSA interactions in comparison to complex 2.
52 citations
TL;DR: Structural polymorphisms were found in the L1 loop regions of H2A.Z.2 in the nucleosomes that are likely to be caused by their flexible nature.
Abstract: The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.
52 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...The structures of the nucleosomes were determined by molecular replacement with Phaser (McCoy et al., 2007) using the coordinates of the human nucleosome structure (PDB entry 3afa; Tachiwana et al., 2010) as the search model....
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...After background subtraction, the intensity was normalized to the intensity of the unbleached region....
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TL;DR: This computer program calculates the orientational variants, the operators and the composition table of a groupoid.
Abstract: A computer program called GenOVa, written in Python, calculates the orientational variants, the operators (special types of misorientations between variants) and the composition table associated with a groupoid structure. The variants can be represented by three-dimensional shapes or by pole figures.
52 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...To the author’s knowledge, there is only one program that simulates the diffraction patterns of variants in transmission electron microscopy (TEM) (Akbay et al., 1994)....
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...The ‘Electron Diffraction’ button will allow the simulation of complex TEM diffraction patterns....
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...The variants can be represented by three-dimensional shapes or by pole figures....
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TL;DR: This work reports the first Hg(2+) selective hydrogelation by 4'-[4-(4-aminophenyl)phenyl]-2,2':6',2''-terpyridine, which showed remarkable response towards specific chemical agents and enabled extensive modulation of the gel morphology.
52 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