Acta Crystallographica Section D: Biological Crystallography最新文献

{"title":"Low-resolution ab initio phasing of Sarcocystis muris lectin SML-2.","authors":"Jürgen J. Müller, N. Lunina, A. Urzhumtsev, E. Weckert, U. Heinemann, V. Lunin","doi":"10.1107/S0108767306095158","DOIUrl":"https://doi.org/10.1107/S0108767306095158","url":null,"abstract":"Structural analysis of the lectin SML-2 faced difficulties when applying standard crystallographic phasing methods. The connectivity-based ab initio phasing method allowed the computation of a 16 A resolution Fourier synthesis and the derivation of primary structural information. It was found that SML-2 crystals have three dimers in the asymmetric part of the unit cell linked by a noncrystallographic symmetry close to translation by (0, 0, 1/3). A clear identification of the noncrystallographic twofold axis explains the space-group transformation from the primitive P2(1)2(1)2(1) to the C-centred C222(1) observed during annealing procedures within an N(2) cryostream for cocrystals of SML-2 and galactose. Related packing considerations predict a possible arrangement of SML-2 molecules in a tetragonal unit cell. Multiple noncrystallographic symmetries and crystal forms provide a basis for further image improvements.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"69 1","pages":"533-40"},"PeriodicalIF":2.2,"publicationDate":"2006-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75637603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biofunctionalization of Nanomaterials. Edited by Challa Kumar. Nanotechnologies for Life Sciences. Volume 1. Pp. xx+366. Weinheim: Wiley–VCH Verlag GmbH Co. KGaA, 2005. Price (hardcover) 139 Euro/220 SFR. ISBN: 3-527-31381-8","authors":"W. Pompe","doi":"10.1107/S0907444906008729","DOIUrl":"https://doi.org/10.1107/S0907444906008729","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"144 1","pages":"465-466"},"PeriodicalIF":2.2,"publicationDate":"2006-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80375624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of the novel alpha-amylase AmyC from Thermotoga maritima.","authors":"A. Dickmanns, M. Ballschmiter, W. Liebl, R. Ficner","doi":"10.2210/pdb2b5d/pdb","DOIUrl":"https://doi.org/10.2210/pdb2b5d/pdb","url":null,"abstract":"alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the hydrolysis of long sugar polymers such as amylose and starch. The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima was determined at 2.2 Angstroms resolution by means of MAD. AmyC lacks sequence similarity to canonical alpha-amylases, which belong to glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity to a group of as yet uncharacterized proteins in COG1543 and is related to glycerol hydrolase family 57 (GH-57). AmyC reveals features that are characteristic of alpha-amylases, such as a distorted TIM-barrel structure formed by seven beta-strands and alpha-helices (domain A), and two additional but less well conserved domains. The latter are domain B, which contains three helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a five-helix region at the C-terminus. Interestingly, despite moderate sequence homology, structure comparison revealed significant similarities to a member of GH-57 with known three-dimensional structure, Thermococcus litoralis 4-glucanotransferase, and an even higher similarity to a structure of an enzyme of unknown function from Thermus thermophilus.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"38 1","pages":"262-70"},"PeriodicalIF":2.2,"publicationDate":"2006-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85952001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure Determination by X-ray Crystallography. By Mark Ladd and Rex Palmer. Pp. xlii + 819. New York: Kluwer Academic/Plenum Publishers, 4th ed., 2003. Price (paperback) GBP 41. ISBN 0-306-47454-9.","authors":"J. Helliwell","doi":"10.1107/S0907444906002010","DOIUrl":"https://doi.org/10.1107/S0907444906002010","url":null,"abstract":"I was very surprised when I was asked by the Editors to write a book review of this Fourth Edition to find that there was no book review for the former editions in the IUCr journals, since ‘Ladd & Palmer’ is a very famous and fundamental book on the subject of crystal structure determination. Therefore, I accepted to write the review, although this edition was published about three years ago. Currently, intensity data are collected automatically within two or three hours using a diffractometer with a twodimensional detector, and the crystal structure can be solved automatically using a convenient software package. The crystal and molecular structures will be drawn on the display of the personal computer. Moreover, all of the crystallographic data and the details of the structure determination are formatted in a crystallographic information file (CIF). It may be possible to submit a report of the crystal structure analysis without any knowledge of crystallography. However, the number of such ideal crystals whose structures are determined automatically is gradually decreasing. We must often analyze the structures of twinned crystals and crystals with disordered groups, solvate molecules or false symmetry. Deep knowledge of crystallography is necessary to overcome such difficult problems. This book is well adapted not only for the beginner but also for the researcher if they want to know the basis of crystallography. In addition to basic crystallography, the following three chapters were added in this edition: X-ray Structure Determination with Powders (chapter 9); Proteins and Macromolecular X-ray Analysis (chapter 10); and Computer-Aided Crystallography (chapter 11). Recently the structure determination of organic and macromolecules using powder diffraction data has been extensively developed. In addition to an explanation of the methods of data collection, indexing and the assignment of the unit cell and space group, an outline of how to build the model structure is described. Not only the reciprocalspace method but also the several directspace methods are explained in detail. Several examples analyzed by powder diffraction are shown. There are many books on protein crystallography. However, I think it is adequate, as the authors suggest in chapter 10, that, although there are definite distinctions between large and small molecules in the crystallographic arena, there is no reason to exclude one from the other, and that there are many advantages of being familiar with both. The chapter includes the methods of crystallization, data collection and processing, phase determination using isomorphous replacement, molecular replacement and multiple-wavelength anomalous dispersion, and structure refinement such as density modification, simulated annealing and least-squares methods. Computing is an essential feature in any modern crystallographic investigation. The basic computation programs for singlecrystal and powder structure determinations are explai","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"1 1","pages":"347-348"},"PeriodicalIF":2.2,"publicationDate":"2006-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82904661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The integration of macromolecular diffraction data.","authors":"A. Leslie","doi":"10.1107/97809553602060000675","DOIUrl":"https://doi.org/10.1107/97809553602060000675","url":null,"abstract":"The objective of any modern data-processing program is to produce from a set of diffraction images a set of indices (hkls) with their associated intensities (and estimates of their uncertainties), together with an accurate estimate of the crystal unit-cell parameters. This procedure should not only be reliable, but should involve an absolute minimum of user intervention. The process can be conveniently divided into three stages. The first (autoindexing) determines the unit-cell parameters and the orientation of the crystal. The unit-cell parameters may indicate the likely Laue group of the crystal. The second step is to refine the initial estimate of the unit-cell parameters and also the crystal mosaicity using a procedure known as post-refinement. The third step is to integrate the images, which consists of predicting the positions of the Bragg reflections on each image and obtaining an estimate of the intensity of each reflection and its uncertainty. This is carried out while simultaneously refining various detector and crystal parameters. Basic features of the algorithms employed for each of these three separate steps are described, principally with reference to the program MOSFLM.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"43 1","pages":"48-57"},"PeriodicalIF":2.2,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85340660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data collection and analysis","authors":"G. Evans, M. A. Walsh","doi":"10.1107/S0907444905040631","DOIUrl":"https://doi.org/10.1107/S0907444905040631","url":null,"abstract":"In this chapter, I present methodological aspects related to data collection and analysis. I present data sources within each case including detailed information with regard to interviewee characteristics. The data collection approach differs between the pilot Case A and the four follow up Cases B‐E. In consequence, I present the longitudinal data collection approach of the pilot case first and continue with the data collection at Cases B‐E. I end with a description of data analysis procedures.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"6 1","pages":"70-78"},"PeriodicalIF":2.2,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78488142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein-Ligand Interactions: Methods and Applications. Edited by G. U. Nienhaus. Pp. xi + 568. Totowa, New Jersey: Humana Press, 2005. Price (hardback) GBP 87.45, USD 135.00. ISBN 1-58829-372-6.","authors":"L. Sawyer","doi":"10.1107/S0907444905029410","DOIUrl":"https://doi.org/10.1107/S0907444905029410","url":null,"abstract":"Since the elucidation of the human genome, and to some extent even before that, the problem of divining the function of a protein given only its amino-acid sequence has been exercising biochemists. With the various post-genomic initiatives to determine the three-dimensional structures of all of the gene products in a given genome, the problem has become ever more pressing – given the structure of a protein, how do you find out what it does? One way is to try to identify the physiologically important molecules with which it interacts in the hope that vital functional clues will emerge. Thus, a wide selection of methods that can be applied to give binding information is essential if the wide differences in structure, solubility and function of ligand and protein are to be accommodated. An additional benefit of this methodology is in the search for new drugs. The book Protein–Ligand Interactions, one in the Methods in Molecular Biology series, sets out a variety of such methods, some well established, others quite new, by which the interactions of proteins with their ligands can be investigated. The 24 chapters, each written by experts in their technique, cover a wide range of methods from the ’wet’ through the biophysical to the computational. While several of the methods will be familiar to most, a few are quite new, or at least their application to biological systems is novel. The general approach, however, of each chapter is the same: a summary, a general introduction explaining the basic principles of the method and the types of problem that can be tackled, the materials and the instrumentation to be used in some typical experiments, which are then described and the results are shown and discussed. Each chapter ends with notes that amplify points made in the body of the text, and of course, an up-to-date reference list. For the established methods, reference to the seminal early literature is also to be found. Several of the chapters cover methods appropriate for the time-resolution of the interaction, necessary to examine intermediate states along a reaction pathway. Thus, chapters on X-ray crystallography, IR, Raman and fluorescence techniques deal with binding to haem proteins, GTPases and lysozyme. High-throughput methods are now seen as essential to the pharmaceutical industry if not elsewhere, but only one chapter deals with a fluorescence screening method based around confocal microscopy such that 1536 different binding experiments carried out in 5 ml drops can be monitored in about half an hour. One aim of this method development is to reduce still further the sample volumes and hence total amounts of both protein and ligand required to provide evidence of binding. It is perhaps to the more unusual methods, however, that many will turn. There is a fascinating chapter on the use of single-molecule fluorescence that detects the conformational fluctuations associated with ligand binding. Equally intriguing is the use of atomic force micros","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"5 1","pages":"1436-1436"},"PeriodicalIF":2.2,"publicationDate":"2005-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79280550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Corrigendum","authors":"Zhi-jie Liu, Dawei Lin, W. Tempel, Jeremy L. Praissman, J. Rose, Bi-Cheng Wang","doi":"10.1107/S0907444905024996","DOIUrl":"https://doi.org/10.1107/S0907444905024996","url":null,"abstract":"Fig. 4 in the article by Liu et al. [(2005), Acta Cryst. D61, 520–527] was labelled incorrectly. A corrected version of the figure is given here. Also in §3.1.3 of the original article the Cr Kα wavelength was given incorrectly. It should be 2.29 A.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"64 1","pages":"1311-1311"},"PeriodicalIF":2.2,"publicationDate":"2005-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0907444905024996","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72502580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (vol D61, pg 613, 2005)","authors":"T. Barends, R. D. Jong, K. Straaten, A. Thunnissen, B. Dijkstra","doi":"10.1107/S0907444905013533","DOIUrl":"https://doi.org/10.1107/S0907444905013533","url":null,"abstract":"Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 A resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found to be tetartohedrally twinned, hampering correct space-group determination and refinement. A refinement protocol was designed to take tetartohedral twinning into account and was successfully applied to refine the structure. The refinement protocol is described and the reasons for the failure of molecular replacement and the success of MAD are discussed in terms of the effects of the tetartohedral twinning.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"42 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2005-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74141451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Redefining Acta D","authors":"E. Baker, Z. Dauter","doi":"10.1107/S0907444904032548","DOIUrl":"https://doi.org/10.1107/S0907444904032548","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"27 1","pages":"1-1"},"PeriodicalIF":2.2,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75193664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}