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Acta Crystallographica Section D: Biological Crystallography最新文献

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Model building and refinement 模型构建和细化
IF 2.2 4区 生物学 Pub Date : 2004-12-01 DOI: 10.1107/S0907444904028586
M. Noble, A. Perrakis
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引用次数: 0
Crystallization and preliminary X-ray analysis of GlcNAc alpha 1,4Gal-releasing endo-beta-galactosidase from Clostridium perfringens. 产气荚膜梭菌GlcNAc α 1,4gal释放内切-半乳糖苷酶的结晶及x射线初步分析
IF 2.2 4区 生物学 Pub Date : 2004-11-25 DOI: 10.2210/pdb1ups/pdb
Lu Deng, Zhi-jie Liu, H. Ashida, Su-chen Li, Yu-Teh Li, P. Horanyi, W. Tempel, J. Rose, Bi-Cheng Wang
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.
独特的梭菌内切- β -半乳糖苷酶(内切- β -gal (GnGa))能够从胃腺黏液细胞型黏液中表达的o-聚糖中释放二糖GlcNAc α 1,4 gal。晶体属于空间群P6(3),晶胞参数a = 160.4, c = 86.1 a。在冷冻条件下,使用同步加速器x射线源,晶体衍射到1.82 a的分辨率。不对称单元包含两个或三个分子。
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引用次数: 1
David Mervyn Blow: a scholar and a gentleman (1931–2004) 大卫·默文·布罗:学者和绅士(1931-2004)
IF 2.2 4区 生物学 Pub Date : 2004-10-01 DOI: 10.1107/S0907444904018384
B. Matthews
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
我与David Blow(摄于1967年)的交往是我职业生涯中的关键一步,更多的是由于运气而不是好的管理。作为一名在澳大利亚从事“小分子”晶体学研究的博士生,我曾写信给马克斯·佩鲁茨(Max Perutz),询问在他的实验室做博士后工作的可能性,并对被接受感到非常兴奋。我和妻子于1963年11月抵达剑桥,就在肯尼迪总统遇刺的同一周。医学研究委员会实验室上方的英国国旗降了半旗,这在任何情况下都是非常罕见的表示尊重的标志,更不用说对一个非公民了。当我向佩鲁茨自我介绍时,他指出,自从我们第一次通信以来,另外两名博士后已经加入了他的小组。他说,如果我仍然想和他一起工作,我可以自由地这样做,但同时他强烈敦促我考虑加入MRC实验室另一个小组的可能性。大卫·布洛的团队就是这样一种可能性。我知道大卫在蛋白质晶体学方面发表过几篇文章,但我认真读过的唯一一篇文章是《通过最小二乘法将平面与一组点联系起来》。这可能是他被引用最少的出版物,但它与我的论文项目有关。然而,我立刻被大卫的个性所吸引,并感觉到我们会相处得很好。此外,大卫的长期合作伙伴迈克尔·罗斯曼即将在普渡大学担任一个新职位。他的技术员芭芭拉·杰弗瑞也即将搬到波士顿地区。我毫不犹豫地加入了大卫的小组。保罗·西格勒(Paul Sigler)在6个月后加入,严格来说,他是一名博士生,尽管他之前在戴维·戴维斯(David Davies)的实验室有丰富的经验,也是一名执业医学博士
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引用次数: 0
Carl-Ivar Brändén (1934–2004)
IF 2.2 4区 生物学 Pub Date : 2004-09-01 DOI: 10.1107/S0907444904018189
Jane Smith
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.
2004年4月28日,科学失去了一位有价值的公民,卡尔·伊瓦尔BraÈndeÂn在与肺癌抗争了18个月后去世。BraÈndeÂn是结构生物学界的杰出成员。卡尔在瑞典北部的拉普兰长大,他的父亲是一所只有一间教室的学校里的老师。他活泼自由的童年让他终生热爱探索和大自然。与此同时,他萌生了一种强烈的愿望,想把自己的视野扩展到寒冷的北方以外,并认定良好的教育是他通往世界其他地方的入场券。这使得他从13岁开始离开家人去上学,最终进入了乌普萨拉大学。卡尔接受的高等科学教育的特点是,无论何时何地,只要发现机会,他就能抓住机会,而且除非遇到重大问题,否则他的智力是不安分的。他开始在乌普萨拉大学学习数学和物理,但由于厌倦了本科物理课程,又受到莱纳斯·鲍林课本的启发,他转向了化学。他早期的一位重要导师是Ingvar Lindqvist教授,他邀请卡尔到他的实验室攻读化学晶体学博士学位。在他的研究与Lindqvist,卡尔共同撰写了最小二乘重构程序的第一个瑞典电子计算机,并使用它来重构几个金属配合物的结构,他已经解决。再次感到无聊,在离开晶体学和化学的边缘,卡尔被生物化学的讲座课程吸引到蛋白质晶体学的新领域。因此,他抓住了一个博士后机会,与英国剑桥MRC实验室的John Kendrew一起开发肌红蛋白的re - nement方法,并于1962年加入了第一代蛋白质晶体学家。在Max Perutz、John Kendrew、Francis Crick、Fred Sanger、Michael Rossmann、David Blow、Sydney Brenner、Aaron Klug、Lubert Stryer、Richard Henderson和其他许多人的陪伴下,Carl经历了分子和结构生物学令人兴奋的早期,并庆祝了诺贝尔奖授予Crick、Watson和Wilkins,以及Perutz和Kendrew。
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引用次数: 0
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. d(GCGAAGC)和d(GCGAAAGC)(四角形)的结构:剪切G.A对的伙伴交换,形成功能的G.AxA.G交叉。
IF 2.2 4区 生物学 Pub Date : 2004-04-01 DOI: 10.1107/S0907444904005104
T. Sunami, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka
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.
已知DNA片段d(GCGAAGC)和d(GCGAAAGC)具有几个非凡的特性。它们的晶体结构分别以1.6 A和1.65 A的分辨率测定。以反平行方式排列的两个七聚体结合形成具有分子双重对称的双聚体。在晶体不对称单元中,有三个结构相同的双相体。在每个双工的两端,两个沃森-克里克G.C对构成茎区。在中心部分,两个剪切的G.A对交叉堆叠在一起,从而使G.A a交叉的两个鸟嘌呤碱基的沃森-克里克和主槽位点暴露在溶剂中,表明其具有功能作用。A(5)残基的腺嘌呤部分位于双链内,夹在A(4)和G(6)残基之间,但没有相互作用的伙伴。为了封闭柜台线上的开放空间,双层结构被强烈弯曲。在d(GCGAAAGC)晶体的不对称单元(四边形)中,只有一个八聚体链。然而,由晶体学上的双重对称相联系的两条链结合形成反平行双相,类似于在八聚体的六方晶体形式中发现的碱基插入双相。有趣的是,目前d(GCGAAGC)的突出结构与d(GCGAAAGC)的碱基插入双工结构之间的显著差异可归因于剪切G.A对的伙伴交换。
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引用次数: 15
Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum. 巴氏梭菌红霉素的金属取代衍生物。
IF 2.2 4区 生物学 Pub Date : 2004-04-01 DOI: 10.1107/S0907444904004998
M. Maher, Maddalena Cross, M. Wilce, J. Guss, A. G. Wedd
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.
制备并结晶了五种不同的金属取代形式的巴氏梭菌红霉素。存在于天然蛋白的Fe(S-Cys)(4)位点上的单个Fe原子依次被Co、Ni、Ga、Cd和Hg交换。所有五种形式的红氧还蛋白都在R3空间群中结晶,并且与天然蛋白同构。Co, Ni和ga取代的蛋白质显示出与Fe形式相似的几何形状的金属位点(有效的D(2d)局部对称),Cd和Hg蛋白质也是如此,但金属-硫键长度显着扩大。对这些结构的了解有助于对这种简单的铁硫电子传递蛋白的功能进行分子理解。
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引用次数: 13
Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu Kα diffraction data only. Erratum 仅利用单晶内部Cu Kα衍射数据中的异常硫信号求解气泡蛋白的结构。勘误表
IF 2.2 4区 生物学 Pub Date : 2004-03-01 DOI: 10.1107/S0907444904002598
J. Olsen, C. Flensburg, O. Olsen, G. Bricogne, A. Henriksen
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.
在Olsen et al. [2004], Acta crystal。作者马库斯·塞博尔德(Marcus Seibold)在不经意间被遗漏了。正确的作者名单在上面。
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引用次数: 23
Structure of the Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase 假定的醌氧化还原酶——大肠杆菌Yhdh的结构
IF 2.2 4区 生物学 Pub Date : 2004-02-26 DOI: 10.2210/PDB1O89/PDB
G. Sulzenbacher, Roig-Zamboni, F. Pagot, Sacha Grisel, A. Salamoni, Christel Valencia, Campanacci, R. Vincentelli, M. Tegoni, H. Eklund, C. Cambillau
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引用次数: 0
Structure of the alpha-amylase inhibitor tendamistat at 0.93 A. α -淀粉酶抑制剂tendamistat在0.93 A时的结构。
IF 2.2 4区 生物学 Pub Date : 2004-01-15 DOI: 10.2210/PDB1OK0/PDB
V. König, L. Vértesy, T. Schneider
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.
蛋白型α -淀粉酶抑制剂tendamistat的晶体结构在100 K下测定,分辨率为0.93 a。所有F > 4 σ (F)反射的最终R因子为9.26%。由全矩阵反演得到的完全占据的蛋白质原子的平均坐标误差为0.018 A。在与靶分子结合的tendamistat的一侧已经确定了多个离散构象的扩展网络。最值得注意的是,残基Tyr15与哺乳动物淀粉酶的富含甘氨酸的环相互作用,其周围有一簇氨基酸侧链,具有两种明确的构象。在这种晶体结构中观察到的柔韧性,以及晶体中晶格接触固定的残基信息,但在之前的核磁共振研究中发现残基是可移动的,这支持了一个模型,在这个模型中,参与结合的大多数残基并不固定在抑制剂的自由形式中,这表明了一种诱导配合类型的结合。
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引用次数: 2
Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid. 变形杆菌过氧化氢酶在基态、氧化态和甲酸络合物下的结构研究。
IF 2.2 4区 生物学 Pub Date : 2003-12-01 DOI: 10.1107/S0907444904001271
P. Andreoletti, A. Pernoud, G. Sainz, P. Gouet, H. Jouve
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.
在2.3 A的分辨率下,解出了奇异变形杆菌过氧化氢酶与抑制剂甲酸配合物的结构。甲酸是过氧化氢酶的关键配体,因为它能够与铁酶反应,产生高自旋铁复合物。或者,它可以与酶促机制的两种瞬态氧化中间体化合物I和II反应。在这项工作中,天然P. mirabilis过氧化氢酶(PMC)和化合物I也在高分辨率(分别为2.0和2.5 A)下从冷冻晶体中测定了结构。对这三种PMC结构的比较表明,甲酸配合物中不存在静息状态下距离血红素铁3.5 a处的水分子,但在化合物I中再次出现。此外,在化合物I形成过程中,在远离活性位点的空腔中观察到溶剂分子的运动,其中甘油分子被硫酸盐取代。这些结果提供了对溶剂分子运动的结构见解,这在酶促反应中可能是重要的。
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引用次数: 11
期刊
Acta Crystallographica Section D: Biological Crystallography
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