Acta Crystallographica Section D: Biological Crystallography最新文献

{"title":"Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu Kα diffraction data only. Erratum","authors":"J. Olsen, C. Flensburg, O. Olsen, G. Bricogne, A. Henriksen","doi":"10.1107/S0907444904002598","DOIUrl":"https://doi.org/10.1107/S0907444904002598","url":null,"abstract":"In the paper by Olsen et al. [(2004), Acta Cryst. D60, 250–255] the author Marcus Seibold was inadvertently missed out. The correct list of authors is given above.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86667252","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 Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase","authors":"G. Sulzenbacher, Roig-Zamboni, F. Pagot, Sacha Grisel, A. Salamoni, Christel Valencia, Campanacci, R. Vincentelli, M. Tegoni, H. Eklund, C. Cambillau","doi":"10.2210/PDB1O89/PDB","DOIUrl":"https://doi.org/10.2210/PDB1O89/PDB","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82448110","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 alpha-amylase inhibitor tendamistat at 0.93 A.","authors":"V. König, L. Vértesy, T. Schneider","doi":"10.2210/PDB1OK0/PDB","DOIUrl":"https://doi.org/10.2210/PDB1OK0/PDB","url":null,"abstract":"The crystal structure of the proteinaceous alpha-amylase inhibitor tendamistat has been determined at 100 K to a resolution of 0.93 A. The final R factor for all reflections with F > 4sigma(F) is 9.26%. The mean coordinate error for fully occupied protein atoms as derived from full-matrix inversion is 0.018 A. An extended network of multiple discrete conformations has been identified on the side of tendamistat that binds to the target molecule. Most notably, residue Tyr15, which interacts with the glycine-rich loop characteristic of mammalian amylases, and a cluster of amino-acid side chains surrounding it are found in two well defined conformations. The flexibility observed in this crystal structure together with information about residues fixed by lattice contacts in the crystal but found to be mobile in a previous NMR study supports a model in which most of the residues involved in binding are not fixed in the free form of the inhibitor, suggesting an induced-fit type of binding.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74293196","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":"Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid.","authors":"P. Andreoletti, A. Pernoud, G. Sainz, P. Gouet, H. Jouve","doi":"10.1107/S0907444904001271","DOIUrl":"https://doi.org/10.1107/S0907444904001271","url":null,"abstract":"The structure of Proteus mirabilis catalase in complex with an inhibitor, formic acid, has been solved at 2.3 A resolution. Formic acid is a key ligand of catalase because of its ability to react with the ferric enzyme, giving a high-spin iron complex. Alternatively, it can react with two transient oxidized intermediates of the enzymatic mechanism, compounds I and II. In this work, the structures of native P. mirabilis catalase (PMC) and compound I have also been determined at high resolution (2.0 and 2.5 A, respectively) from frozen crystals. Comparisons between these three PMC structures show that a water molecule present at a distance of 3.5 A from the haem iron in the resting state is absent in the formic acid complex, but reappears in compound I. In addition, movements of solvent molecules are observed during formation of compound I in a cavity located away from the active site, in which a glycerol molecule is replaced by a sulfate. These results give structural insights into the movement of solvent molecules, which may be important in the enzymatic reaction.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76097103","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":"Acta D ten years on","authors":"E. Baker, Z. Dauter","doi":"10.1107/S0907444903027069","DOIUrl":"https://doi.org/10.1107/S0907444903027069","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75307816","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":"Unravelling the structural chemistry of the colouration mechanism in lobster shell.","authors":"N. Chayen, M. Cianci, J. Grossmann, J. Habash, J. Helliwell, G. Nneji, J. Raftery, P. Rizkallah, P. F. Zagalsky","doi":"10.1107/S0907444905019621","DOIUrl":"https://doi.org/10.1107/S0907444905019621","url":null,"abstract":"Biochemistry, biological crystallography, spectroscopy, solution X-ray scattering and microscopy have been applied to study the molecular basis of the colouration in lobster shell. This article presents a review of progress concentrating on recent results but set in the context of more than 50 years of work. The blue colouration of the carapace of the lobster Homarus gammarus is provided by a multimolecular carotenoprotein, alpha-crustacyanin. The complex is a 16-mer of five different subunits each binding the carotenoid, astaxanthin (AXT). A breakthrough in the structural studies came from the determination of the structure of beta-crustacyanin (protein subunits A1 with A3 with two shared bound astaxanthins). This was solved by molecular replacement using apocrustacyanin A1 as the search motif. A molecular movie has now been calculated by linear interpolation based on these two 'end-point' protein structures, i.e. apocrustacyanin A1 and A1 associated with the two astaxanthins in beta-crustacyanin, and is presented with this paper. This movie highlights the structural changes forced upon the carotenoid on complexation. In contrast, the protein-binding site remains relatively unchanged in the binding region, but there is a large conformational change occurring in a more remote surface-loop region. It is suggested here that this loop could be important in complexation of AXT and contributes to the spectral properties. Also presented here is the first observation of single-crystal diffraction of the full 'alpha-crustacyanin' complex comprising 16 protein subunits and 16 bound AXT molecules (i.e eight beta-crustacyanins) at 5 A resolution. Optimization of crystallization conditions is still necessary as these patterns show multiple crystallite character, however, 10 A resolution single-crystal diffraction has now been achieved. Provision of the new SRS MPW 10 and SRS MPW 14 beamline robotic systems will greatly assist in the surveying of the many alpha-crustacyanin crystallization trials that are being made. New solution X-ray scattering (SXS) measurements of beta- and alpha-crustacyanin are also presented. The beta-crustacyanin SXS data serve to show how the holo complex fits the SXS curve, whereas the apocrustacyanin A1 homodimer from the crystal data naturally does not. Reconstructions of alpha-crustacyanin were accomplished from its scattering-profile shape. The most plausible ultrastructure, based on a fourfold symmetry constraint, was found to be a stool with four legs. The latter is compared with published electron micrographs. A detailed crystal structure of alpha-crustacyanin is now sought in order to relate the full 150 nm bathochromic shift of AXT to that complete molecular structure, compared with the 100 nm achieved by the beta-crustacyanin protein dimer alone. Rare lobster colourations have been brought to attention as a result of this work and are discussed in an appendix.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76313435","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":"Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation.","authors":"Cheng Yang, J. Pflugrath, D. A. Courville, C. Stence, J. Ferrara","doi":"10.1107/S0108767304097612","DOIUrl":"https://doi.org/10.1107/S0108767304097612","url":null,"abstract":"Anomalous scattering with soft X-ray radiation opens new possibilities in phasing for macromolecular crystallography. Anomalous scattering from S atoms collected on an in-house chromium radiation source (lambda = 2.29 A) was used to phase the X-ray diffraction data of thaumatin (22 kDa) and trypsin (24 kDa) crystals. The contribution to the anomalous term, Deltaf\" = 1.14 e(-), from sulfur for Cr Kalpha radiation is doubled compared with that for Cu Kalpha radiation, Deltaf\" = 0.56 e(-). The direct-methods programs RANTAN or SHELXD successfully found sulfur positions using data sets with resolution limited to 3.5 A. The statistical phasing program SHARP was used to produce the electron-density maps using the sulfur anomalous signal alone at low resolution ( approximately 3.5 A). An interpretable electron-density map for each structure was obtained solely from the phases derived from single-wavelength anomalous dispersion (SAD) data obtained using Cr Kalpha radiation. Much fewer data (that is, lower redundancy) are required for this sulfur SAD phasing procedure compared with the highly redundant data reported in the sulfur SAD phasing procedure with Cu Kalpha radiation. Cr Kalpha radiation can also improve the strength of anomalous scattering of many other intrinsic elements in macromolecules, such as calcium, zinc and phosphorus, because of the increased Deltaf\". Furthermore, the anomalous scattering of selenium is increased substantially from 1.14 e(-) with Cu Kalpha radiation to 2.28 e(-) with Cr Kalpha radiation. In order to measure the small Bijvoet differences accurately, several devices were developed for the experiment, including an Osmic Confocal MaxFlux optic optimized for Cr Kalpha radiation, a helium path and a beam stop. In the cases studied here, radiation damage to the samples and reduction of anomalous signal were observed in some long exposure time data sets. Therefore, an adequate data-collection strategy to maximize the completeness in a short scan range was used in subsequent data collections. The results show that the anomalous signal of S atoms can be collected quickly. Since the absorption of solvent and the loop may no longer be negligible with Cr Kalpha radiation, the orientation of the crystal and exposure time were taken into account in order to minimize the effects of radiation damage and absorption. This experimental study shows that using Cr Kalpha radiation from an in-house rotating-anode X-ray generator can provide sufficient phasing power from sulfur anomalous signals to routinely phase protein diffraction data.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77751385","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":"Hemoglobin Disorders, Molecular Methods and Protocols. Edited by Ronald L Nagel. Humana Press, 2003, 300 pp. Price USD 99.50. ISBN 0-89603-962-5.","authors":"M. Hart","doi":"10.1107/S090744490301179X","DOIUrl":"https://doi.org/10.1107/S090744490301179X","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75904336","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":"Outline of Crystallography for Biologists. By David Blow. Oxford University Press, 2002. Price GBP 25 (paperback). ISBN-0-19-851051-9.","authors":"R. Sweet","doi":"10.1107/S0907444903006735","DOIUrl":"https://doi.org/10.1107/S0907444903006735","url":null,"abstract":"Crystallographic techniques provided the original de®nition for the term Structural Biology. They are now the pre-eminent tool for determining the structures of biological molecules with masses less than 500 00 Da, and are applicable up into the low millions. Biologists not only read the papers, but also are beginning to do the experimental work, with or without a license. David Blow's new book provides a beginner's Operator's Manual for the method. Blow himself described the book as `crystallography without maths', and that describes the outer layer well. However, because the method is so inherently mathematical, he couldn't resist adding mathematical details in grey boxes. There are copious warnings to the mathematically disinclined to stay away from the equations that lurk in these boxes, but promises to those who want the detail that there are riches to be found there. Both the warnings and the promises are well placed. In the ®rst place, no apologies are made for writing the mathematics in the formal fashion that it deserves. The grey boxes are not for those who are uncomfortable with integral signs or complex exponentials. On the other hand, the great bulk of the necessary mathematics of crystallography is laid out, concisely and clearly. Concise and clear really describes the bulk of the book too. Each topic is developed from a number of simple ideas in a logical development that is easy to follow, if one pays attention. There are copious illustrations, probably an average of one per page, that amplify the text. There are classical images: von Laue's original diffraction image, Taylor and Lipson's rubber ducky with its diffraction pattern, or Harrison's 1980 diagram showing the difference between the T = 1 and T = 3 icosahedral surface lattice of a virus. Blow uses numerous examples from the literature and his students' theses to amplify points, and some ®gures come from these. Then there are many diagrams created just for this volume. The book is divided roughly in half to reveal Fundamentals ®rst, then Practice. The subject matter nicely surveys the ®eld. Images and X-rays, Crystals and symmetry, Waves, Diffraction, and Diffraction by crystals comprise the Fundamentals section. The Practice section includes Intensity measurement, Isomorphous replacement, Anomalous scattering, Molecular replacement, Density modi®cation, Electrondensity maps, Structural re®nement and Accuracy of the model. Because Blow himself played such an important role in structure solving (the Rossmann/Blow rotation and translation functions, and the Blow/Crick method for ®nding the `best' phase from isomorphous replacement), these sections of the book are especially powerful. In summary, this is a book that can be read either by a practitioner who would like some entertainment, or by a novice who might bene®t from illumination. Because the exposition is so logical, the thread can be picked up at any point and a naõ Ève reader can get value on a particular topic and n","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74919201","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":"DNA and beyond","authors":"E. Baker, Z. Dauter","doi":"10.1107/S0907444903005900","DOIUrl":"https://doi.org/10.1107/S0907444903005900","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2003-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86811553","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}