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 structure of 'metal-free' glucose isomerase of Streptomyces albus strain number YT ATCC 21132 has been analysed and refined at 1.65 A to a final R factor of 14.1%.
Abstract: The structure of 'metal-free' glucose isomerase of Streptomyces albus strain number YT ATCC 21132 has been analysed and refined at 1.65 A. The space group is I222, with cell dimensions a = 93.9 (1), b = 99.7 (1) and c = 102.9 (1) A, and there is one monomer of the tetrameric molecule per asymmetric unit. The data were recorded from two crystals of the protein using synchrotron radiation from the EMBL beamline X11 at DESY, Hamburg. Data were recorded with an imaging plate scanner designed and built in the EMBL Hamburg outstation. The total data-collection time was less than 12 h and the processing of all data took less than 2 days. The coordinates of the Arthrobacter glucose isomerase refined at a resolution of 2.5 A were used as a starting model. The structure of the protein and of 445 associated water molecules in the asymmetric unit were refined by restrained least-squares minimization using all data between 8 and 1.65 A to a final R factor of 14.1%.
31 citations
TL;DR: It can be inferred from the locations of strictly conserved amino acids in the polypeptide chain that the maintenance of the overall conformation of the PPIase domains of FKBPs is essential for the P PIase activity.
Abstract: FKBP52 is a member of the FK506-binding protein family (FKBPs). The N-terminal domain of FKBP52 (FKBP52-N; residues 1-140) is responsible for peptidyl-prolyl isomerase activity and binding of FK506. Here, the crystal structure of FKBP52-N has been determined by molecular replacement to 2.4 A. FKBP52-N is defined by a six-stranded antiparallel beta-sheet wrapping with a right-handed twist around a short alpha-helix, an architecture similar to that of FKBP12. FKBP52-N is able to bind FK506 in a similar way to FKBP12. The variability in two loop regions (residues 70-76 and 108-127) is the principal reason for the specificity differences between FKBP52-N and FKBP12. The Pro120 change corresponding to Gly89 in FKBP12 limits the conformational adaptation between the loop (residues 108-127) and FK506 and decreases the FK506 affinity, while the Lys121 substitution corresponding to Ile90 of FKBP12 destroys a key interaction between FKBP52-N and calcineurin. It can be inferred from the locations of strictly conserved amino acids in the polypeptide chain that the maintenance of the overall conformation of the PPIase domains of FKBPs is essential for the PPIase activity. The N-terminal region and beta-sheets of FKBP52-N forms a hydrophobic patch which may be responsible for the binding of target proteins such as dynein or PAHX.
31 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...2(a), 2(b), 3 and 5 were generated using the programs MOLSCRIPT (Kraulis, 1991) or BOBSCRIPT (Esnouf, 1997). by 1.4 AÊ towards the bottom of the pocket in subunit A, thus making the binding cavity a little deeper compared with molecule B. Similar differences are also observed when the structures of…...
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...2(a), 2(b), 3 and 5 were generated using the programs MOLSCRIPT (Kraulis, 1991) or BOBSCRIPT (Esnouf, 1997). by 1.4 AÊ towards the bottom of the pocket in subunit A, thus making the binding cavity a little deeper compared with molecule B. Similar differences are also observed when the structures of free and complexed FKBP12 are compared....
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TL;DR: SynchWeb significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography.
Abstract: SynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.
31 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Edge scans are displayed with the resulting CHOOCH (Evans & Pettifer, 2001) plot if successful, along with the associated f 0 and f 00 values at the peak and inflection points of the absorption edge....
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TL;DR: Speciation modeling calculations suggest that, under serum conditions, apoTf is probably the primary metal ion binder, even in the presence of the most stable V(V) carrier ligands hpno and maltol and HSA plays a negligible role in V( V) binding.
Abstract: The speciations of two drug candidate ligands, 2-hydroxypyridine-N-oxide (Hhpno) and 2-mercaptopyridine-N-oxide (Hmpno), with vanadate (VV) were determined at 25.0 °C and 0.20 mol dm−3 KCl by pH-metric and 51V-NMR methods. At pH 7.4, the two predominant compounds with both ligands are the VO2L2 and VO2L(OH). NH4[VO2(hpno)2]·3H2O was prepared in solid form, and its crystal structure was determined by X-ray diffraction. The stabilities of the complexes VO2L2 of five drug candidate ligands were compared at pH 7.4. In view of the stability sequence hpno > maltol ∼ hdp (Hhdp: 3-hydroxy-1,2-dimethyl-4-pyridinone) ≫ mpno > picolinic acid, the first two of these ligands were chosen for equilibrium studies with apotransferrin (apoTf) competition. The VV-apoTf stability constants (log K1 = 6.03 ± 0.10; log K2 = 5.46 ± 0.18) determined by 51V-NMR spectroscopy were confirmed by ultrafiltration. Both methods proved that there seems to be no hydrogencarbonate–vanadate competition for the apoTf anion-binding positions. The other potential high molecular mass VV binder in the serum is human serum albumin (HSA). As no interaction was detected by 51V-NMR spectroscopy or fluorimetry, the binding properties of HSA were quantified on the basis of literature data. As a final conclusion, speciation modeling calculations suggest that, under serum conditions, apoTf is probably the primary metal ion binder, even in the presence of the most stable VV carrier ligands hpno and maltol and HSA plays a negligible role in VV binding.
31 citations
TL;DR: In this article, a methodology for combining three-dimensional tomographic data has been developed for combining multi-modal data sets acquired via multiple techniques for the quantitative analysis of structure, chemistry and phase information.
Abstract: Recently, techniques for the acquisition of three-dimensional tomographic and four-dimensional time-resolved data sets have emerged, allowing for the analysis of mm3 volumes of material with nm-scale resolution. The ability to merge multi-modal data sets acquired via multiple techniques for the quantitative analysis of structure, chemistry and phase information is still a significant challenge. Large three-dimensional data sets have been acquired by time-resolved diffraction contrast tomography (DCT) and a new TriBeam tomography technique with high spatial resolution to address grain growth in strontium titanate. A methodology for combining three-dimensional tomographic data has been developed. Algorithms for the alignment of orientation reference frames, unification of sampling grids and automated grain matching have been integrated, and the resulting merged data set permits the simultaneous analysis of all tomographic data on a voxel-by-voxel and grain-by-grain basis. Quantitative analysis of merged data sets collected using DCT and TriBeam tomography shows that the spatial resolution of the DCT technique is limited near grain boundaries and the sample edge, resolving grains down to 10 µm diameter for the reconstruction method used. While the TriBeam technique allows for higher-resolution analysis of boundary plane location, it is a destructive tomography approach and can only be employed at the conclusion of a four-dimensional experiment.
31 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...X-ray DCT is a nondestructive three-dimensional tomography technique for imaging crystalline microstructures and the reconstruction of grain shape and orientation (Poulsen et al., 2001; Ludwig et al., 2008; Johnson et al., 2008; Ludwig, Reischig et al., 2009)....
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...…and diffraction contrast data were reconstructed using algorithms that are described elsewhere (Reischig et al., 2013; Kak & Slaney, 1988; Johnson et al., 2008; Cloetens et al., 1997), and have been used to reconstruct grain information in materials such as alumina (Gonzalez et al.,…...
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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.
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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.
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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'.
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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.
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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