Acta Crystallographica Section D: Biological Crystallography最新文献

{"title":"Model building and refinement","authors":"M. Noble, A. Perrakis","doi":"10.1107/S0907444904028586","DOIUrl":"https://doi.org/10.1107/S0907444904028586","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"22 1","pages":"0-0"},"PeriodicalIF":2.2,"publicationDate":"2004-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88717045","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":"Crystallization and preliminary X-ray analysis of GlcNAc alpha 1,4Gal-releasing endo-beta-galactosidase from Clostridium perfringens.","authors":"Lu Deng, Zhi-jie Liu, H. Ashida, Su-chen Li, Yu-Teh Li, P. Horanyi, W. Tempel, J. Rose, Bi-Cheng Wang","doi":"10.2210/pdb1ups/pdb","DOIUrl":"https://doi.org/10.2210/pdb1ups/pdb","url":null,"abstract":"The unique clostridial endo-beta-galactosidase (Endo-beta-Gal(GnGa)) capable of releasing the disaccharide GlcNAc alpha 1,4Gal from O-glycans expressed in the gastric gland mucous cell-type mucin has been crystallized. The crystal belongs to space group P6(3), with unit-cell parameters a = 160.4, c = 86.1 A. Under cryocooled conditions and using a synchrotron X-ray source, the crystals diffract to 1.82 A resolution. The asymmetric unit contains two or three molecules.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"8 1","pages":"537-8"},"PeriodicalIF":2.2,"publicationDate":"2004-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76307113","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":"David Mervyn Blow: a scholar and a gentleman (1931–2004)","authors":"B. Matthews","doi":"10.1107/S0907444904018384","DOIUrl":"https://doi.org/10.1107/S0907444904018384","url":null,"abstract":"My association with David Blow (photograph ca 1967), which was a pivotal step in my career, was due more to good luck than good management. As a PhD student in Australia working in`small molecule' crystallography, I had written to Max Perutz asking about the possibility of doing postdoctoral work in his laboratory and was very excited to be accepted. My wife and I arrived in Cambridge in November 1963, the same week that President Kennedy had been assassinated. The Union Jack over the Medical Research Council laboratory was ¯ying at half-mast, an extraordinarily rare sign of respect under any circumstances, let alone for a non-citizen. When I introduced myself to Perutz he indicated that, since we had ®rst corresponded, two other postdoctoral associates had already joined his group. If I still wanted to work with him I would be free to do so, he said, but at the same time he strongly urged me to consider the possibility of joining another group within the MRC laboratory. David Blow's group was one such possibility. I was aware that David had several publications in protein crystallography but the only article of his that I had read with any care was the notèTo ®t a plane to a set of points by least squares'. It is possibly his least-quoted publication but one which was relevant to my thesis project. I was, however, immediately taken with David's personality and sensed that we would get on well together. Furthermore, Michael Rossmann, who had been David's long-standing collaborator, was about to assume a new position at Purdue University. Also his technician, Barbara Jeffery, was about to move to the Boston area. I had little hesitation in joining David's group. Paul Sigler was to join six months later, technically as a PhD student although with substantial prior experience in David Davies' laboratory and as a practising MD","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"24 1","pages":"1695-1697"},"PeriodicalIF":2.2,"publicationDate":"2004-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79320137","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":"Carl-Ivar Brändén (1934–2004)","authors":"Jane Smith","doi":"10.1107/S0907444904018189","DOIUrl":"https://doi.org/10.1107/S0907444904018189","url":null,"abstract":"Science lost a valued citizen on 28 April 2004 when Carl-Ivar BraÈndeÂn succumbed to lung cancer following an 18-month battle. BraÈndeÂn was a prominent member of the structural biology community. Carl grew up in Lapland in northern Sweden, where his father was the teacher in a one-room schoolhouse. His active and free childhood instilled a life-long love of exploration and nature. At the same time he developed a strong desire to expand his horizons beyond the frozen north, and decided that a good education was his ticket to rest of the world. This led him, from age 13 onward, to schooling away from his family and eventually to Uppsala University. Carl's higher education in science was characterized by an ability to take opportunities where and when he found them and by an intellect that was restless unless challenged with an important problem. He began studying mathematics and physics at Uppsala University, but, bored by the undergraduate physics curriculum and inspired by Linus Pauling's texts, he switched to chemistry. An early and important mentor was Professor Ingvar Lindqvist, who invited Carl into his laboratory for PhD studies in chemical crystallography. During his studies with Lindqvist, Carl co-authored a least-squares re®nement program for the ®rst Swedish electronic computer and used it to re®ne the structures of several metal coordination complexes he had solved. Again bored and on the verge of leaving both crystallography and chemistry, Carl was enticed to the new ®eld of protein crystallography by a lecture course in biochemistry. Thus, he leapt at a postdoctoral opportunity to develop re®nement methods for myoglobin with John Kendrew at the MRC laboratory in Cambridge, UK, where in 1962 joined the ®rst generation of protein crystallographers. In the company of Max Perutz, John Kendrew, Francis Crick, Fred Sanger, Michael Rossmann, David Blow, Sydney Brenner, Aaron Klug, Lubert Stryer, Richard Henderson and many others, Carl experienced the heady early days of molecular and structural biology and celebrated the Nobel prizes to Crick, Watson and Wilkins, and to Perutz and Kendrew.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"56 1","pages":"1509-1511"},"PeriodicalIF":2.2,"publicationDate":"2004-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78849431","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":"Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.","authors":"T. Sunami, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka","doi":"10.1107/S0907444904005104","DOIUrl":"https://doi.org/10.1107/S0907444904005104","url":null,"abstract":"The DNA fragments d(GCGAAGC) and d(GCGAAAGC) are known to exhibit several extraordinary properties. Their crystal structures have been determined at 1.6 and 1.65 A resolution, respectively. Two heptamers aligned in an antiparallel fashion associate to form a duplex having molecular twofold symmetry. In the crystallographic asymmetric unit, there are three structurally identical duplexes. At both ends of each duplex, two Watson-Crick G.C pairs constitute the stem regions. In the central part, two sheared G.A pairs are crossed and stacked on each other, so that the stacked two guanine bases of the G.AxA.G crossing expose their Watson-Crick and major-groove sites into solvent, suggesting a functional role. The adenine moieties of the A(5) residues are inside the duplex, wedged between the A(4) and G(6) residues, but there are no partners for interactions. To close the open space on the counter strand, the duplex is strongly bent. In the asymmetric unit of the d(GCGAAAGC) crystal (tetragonal form), there is only one octamer chain. However, the two chains related by the crystallographic twofold symmetry associate to form an antiparallel duplex, similar to the base-intercalated duplex found in the hexagonal crystal form of the octamer. It is interesting to note that the significant difference between the present bulge-in structure of d(GCGAAGC) and the base-intercalated duplex of d(GCGAAAGC) can be ascribed to a switching of partners of the sheared G.A pairs.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"2 1","pages":"422-31"},"PeriodicalIF":2.2,"publicationDate":"2004-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89928391","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":"Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum.","authors":"M. Maher, Maddalena Cross, M. Wilce, J. Guss, A. G. Wedd","doi":"10.1107/S0907444904004998","DOIUrl":"https://doi.org/10.1107/S0907444904004998","url":null,"abstract":"Five different metal-substituted forms of Clostridium pasteurianum rubredoxin have been prepared and crystallized. The single Fe atom present in the Fe(S-Cys)(4) site of the native form of the protein was exchanged in turn for Co, Ni, Ga, Cd and Hg. All five forms of rubredoxin crystallized in space group R3 and were isomorphous with the native protein. The Co-, Ni- and Ga-substituted proteins exhibited metal sites with geometries similar to that of the Fe form (effective D(2d) local symmetry), as did the Cd and Hg proteins, but with a significant expansion of the metal-sulfur bond lengths. A knowledge of these structures contributes to a molecular understanding of the function of this simple iron-sulfur electron-transport protein.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"18 1","pages":"298-303"},"PeriodicalIF":2.2,"publicationDate":"2004-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75021830","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":"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":"40 1","pages":"250-255"},"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":"94 1","pages":"1855"},"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":"17 1","pages":"1737-43"},"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":"47 1","pages":"2163-8"},"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}