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Crystallization and preliminary X-ray study of the deaminase AmnE from Pseudomonas sp. AP-3. Corrigendum 假单胞菌AP-3脱氨酶AmnE的结晶及x射线初步研究。应改正的错误
IF 0.9 4区 生物学 Pub Date : 2013-10-31 DOI: 10.1107/S1744309113029321
Dan Yu, Yongji Jiang, Jianfeng Hou, Shuai Chen, Guofang Zhang, Xiang Liu, Hui Dong, Bo Yu
A correction is made to the article by Yu et al. (2013). Acta Cryst. F69, 812–814.
Yu等人(2013)对文章进行了更正。Acta结晶。F69, 812 - 814。
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引用次数: 0
Crystallization and preliminary X-ray study of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4. Corrigendum 热厌氧菌腾根菌MB4耐热丙氨酸消旋酶的结晶及x射线初步研究。应改正的错误
IF 0.9 4区 生物学 Pub Date : 2013-10-31 DOI: 10.1107/S1744309113029114
Hui Dong, Shujing Xu, Xiaoyu Lu, Guangzheng He, Ranran Zhao, Shuai Chen, Sheng Fu, J. Ju
A correction is made to the article by Dong et al. (2013). Acta Cryst. F69, 660–662.
Dong et al.(2013)对文章进行了更正。Acta结晶。F69, 660 - 662。
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引用次数: 1
Production and crystallization of α-phosphoglucomutase from Lactococcus lactis. Corrigendum 乳酸乳球菌α-磷酸葡萄糖糖化酶的产生和结晶。应改正的错误
IF 0.9 4区 生物学 Pub Date : 2013-10-31 DOI: 10.1107/S1744309113029126
P. Nogly, Rute Castro, Matteo de Rosa, A. R. Neves, Helena Santos, Margarida Archer
A correction is made to the article by Nogly et al. (2012). Acta Cryst. F68, 1113–1115.
Nogly等人(2012)对文章进行了更正。Acta结晶。F68, 1113 - 1115。
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引用次数: 0
Identification, characterization and preliminary X-ray diffraction analysis of the rolling-circle replication initiator protein from plasmid pSTK1. 质粒 pSTK1 中滚动圈复制启动蛋白的鉴定、表征和初步 X 射线衍射分析。
IF 0.9 4区 生物学 Pub Date : 2013-10-01 Epub Date: 2013-09-28 DOI: 10.1107/S1744309113023828
Stephen B Carr, Lauren B Mecia, Simon E V Phillips, Christopher D Thomas

Antibiotic resistance in bacterial pathogens poses an ever-increasing risk to human health. In antibiotic-resistant strains of Staphylococcus aureus this resistance often resides in extra-chromosomal plasmids, such as those of the pT181 family, which replicate via a rolling-circle mechanism mediated by a plasmid-encoded replication initiation protein. Currently, there is no structural information available for the pT181-family Rep proteins. Here, the crystallization of a catalytically active fragment of a homologous replication initiation protein from the thermophile Geobacillus stearothermophilus responsible for the replication of plasmid pSTK1 is reported. Crystals of the RepSTK1 fragment diffracted to a resolution of 2.5 Å and belonged to space group P2₁2₁2₁.

细菌病原体的抗生素耐药性对人类健康造成的威胁日益严重。在金黄色葡萄球菌的抗生素耐药菌株中,这种耐药性通常存在于染色体外的质粒中,如 pT181 家族的质粒,它们通过质粒编码的复制启动蛋白介导的滚圆机制进行复制。目前,还没有关于 pT181 家族 Rep 蛋白的结构信息。本文报告了嗜热菌 Geobacillus stearothermophilus 中负责复制质粒 pSTK1 的同源复制起始蛋白催化活性片段的结晶。RepSTK1 片段的晶体衍射分辨率为 2.5 Å,属于空间群 P2₁2₁2₁。
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引用次数: 0
Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I. 调控限制性修饰系统 Esp1396I 的 DNA 蛋白复合物结构分析。
IF 0.9 4区 生物学 Pub Date : 2013-09-01 Epub Date: 2013-08-19 DOI: 10.1107/S174430911302126X
Richard N A Martin, John E McGeehan, Neil J Ball, Simon D Streeter, Sarah-Jane Thresh, G G Kneale

The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical and crystallographic studies have shown molecular details of how the controller protein binds to the operator sites with very different affinities. Here, two protein-DNA co-crystal structures containing portions of unbound DNA from native operator sites are reported. The DNA in both complexes shows significant distortion in the region between the conserved symmetric sequences, similar to that of a DNA duplex when bound by the controller protein (C-protein), indicating that the naked DNA has an intrinsic tendency to bend when not bound to the C-protein. Moreover, the width of the major groove of the DNA adjacent to a bound C-protein dimer is observed to be significantly increased, supporting the idea that this DNA distortion contributes to the substantial cooperativity found when a second C-protein dimer binds to the operator to form the tetrameric repression complex.

II 型限制性修饰(RM)系统的控制蛋白 Esp1396I 与甲基转移酶和内切酶基因上游的三个不同 DNA 操作序列结合,以调控它们的表达。先前的生物物理和晶体学研究显示了控制蛋白如何以非常不同的亲和力与操作者位点结合的分子细节。本文报告了两种蛋白质-DNA 共晶体结构,其中包含来自原生操作者位点的未结合 DNA 部分。这两种复合物中的 DNA 在保守对称序列之间的区域显示出明显的扭曲,类似于 DNA 双链与控制蛋白(C 蛋白)结合时的扭曲,表明裸 DNA 在未与 C 蛋白结合时具有内在的弯曲趋势。此外,还观察到与结合的 C 蛋白二聚体相邻的 DNA 主沟宽度明显增加,这支持了这样一种观点,即当第二个 C 蛋白二聚体与操作者结合形成四聚体抑制复合物时,DNA 的这种扭曲会产生巨大的合作作用。
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引用次数: 0
Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. 利用 X 射线自由电子激光器对环境温度下液体悬浮液中的 30S 核糖体亚基微晶体进行串行飞秒 X 射线衍射。
IF 0.9 4区 生物学 Pub Date : 2013-09-01 Epub Date: 2013-08-19 DOI: 10.1107/S174430911302099X
Hasan Demirci, Raymond G Sierra, Hartawan Laksmono, Robert L Shoeman, Sabine Botha, Thomas R M Barends, Karol Nass, Ilme Schlichting, R Bruce Doak, Cornelius Gati, Garth J Williams, Sébastien Boutet, Marc Messerschmidt, Gerwald Jogl, Albert E Dahlberg, Steven T Gregory, Michael J Bogan

High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.

通过 X 射线晶体学确定的高分辨率核糖体结构为翻译机制提供了重要的见解。迄今为止,此类研究一直依赖于低温保存的大型核糖体晶体,以减少辐射损伤。本文介绍了利用 X 射线自由电子激光器(XFEL)进行串行飞秒 X 射线晶体学(SFX)的应用,以获得环境温度下液态悬浮液中核糖体微晶体的衍射数据。30S 核糖体亚基微晶体的衍射分辨率超过 6 Å,证明了使用 SFX 进行核糖体结构研究的可行性。在接近生理温度下收集衍射数据的能力有望为核糖体及其功能复合物的结构动态提供基础性见解。
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引用次数: 0
Purification, crystallization and preliminary X-ray diffraction analysis of the 23S rRNA methyltransferase RlmJ from Escherichia coli. 大肠杆菌 23S rRNA 甲基转移酶 RlmJ 的纯化、结晶和初步 X 射线衍射分析。
IF 0.9 4区 生物学 Pub Date : 2013-09-01 Epub Date: 2013-08-19 DOI: 10.1107/S1744309113020289
Avinash S Punekar, Maria Selmer

Methyltransferase RlmJ uses the cofactor S-adenosylmethionine to methylate the exocyclic nitrogen N6 of nucleotide A2030 in 23S rRNA during ribosome assembly in Escherichia coli. RlmJ with a C-terminal hexahistidine tag was overexpressed in E. coli and purified as a monomer using Ni(2+)-affinity and size-exclusion chromatography. The recombinant RlmJ was crystallized using the sitting-drop vapour-diffusion method and a full data set was collected to 1.85 Å resolution from a single apo crystal. The crystals belonged to space group P2(1), with unit-cell parameters a = 46.9, b = 77.8, c = 82.5 Å, β = 104°. Data analysis suggested two molecules per asymmetric unit and a Matthews coefficient of 2.20 Å(3) Da(-1).

甲基转移酶 RlmJ 在大肠杆菌核糖体组装过程中利用辅助因子 S-腺苷蛋氨酸将 23S rRNA 中核苷酸 A2030 的外环氮 N6 甲基化。在大肠杆菌中过表达了带有 C 端六组氨酸标签的 RlmJ,并使用 Ni(2+)- 亲和层析和尺寸排阻层析将其纯化为单体。重组 RlmJ 采用坐滴蒸发扩散法结晶,并从单个 apo 晶体中收集了分辨率为 1.85 Å 的全套数据。晶体属于空间群 P2(1),单位晶胞参数 a = 46.9、b = 77.8、c = 82.5 Å、β = 104°。数据分析表明,每个不对称单元有两个分子,马修斯系数为 2.20 Å(3) Da(-1)。
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引用次数: 0
Expression, purification, crystallization and preliminary X-ray studies of Lactobacillus jensenii enolase. Corrigendum 延寿乳杆菌烯醇化酶的表达、纯化、结晶及x射线初步研究。应改正的错误
IF 0.9 4区 生物学 Pub Date : 2013-08-19 DOI: 10.1107/S1744309113012001
P. Harris, K. Raghunathan, R. Spurbeck, C. Arvidson, D. Arvidson
A correction is made to the article by Harris et al. [(2010) Acta Cryst. F66, 938–940].
对Harris等人的文章进行了更正[(2010)Acta crystal。]F66, 938 - 940]。
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引用次数: 0
Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium. 巨型芽孢杆菌四吡咯生物合成酶卟啉原脱氨酶的结晶和初步 X 射线表征。
IF 0.9 4区 生物学 Pub Date : 2013-08-01 Epub Date: 2013-07-27 DOI: 10.1107/S1744309113018526
N Azim, E Deery, M J Warren, P Erskine, J B Cooper, S P Wood, M Akhtar

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.

卟啉原脱氨酶(PBGD;羟甲基比兰合成酶;EC 2.5.1.61)催化四吡咯生物合成途径的早期步骤,在该步骤中,四分子单吡咯卟啉原缩合成线性四吡咯。该酶具有一个二吡咯烷辅助因子,该辅助因子通过硫醚桥与一个不变的半胱氨酸残基共价连接。在大肠杆菌中表达 His 标记形式的巨型芽孢杆菌 PBGD 使该物种的酶得以结晶并进行了初步的高分辨率 X 射线分析。
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引用次数: 0
The putative small terminase from the thermophilic dsDNA bacteriophage G20C is a nine-subunit oligomer. 嗜热dsDNA噬菌体G20C的推定小终结酶是一个九亚基寡聚体。
IF 0.9 4区 生物学 Pub Date : 2013-08-01 Epub Date: 2013-07-27 DOI: 10.1107/S1744309113017016
Juan Loredo-Varela, Maria Chechik, Vladimir M Levdikov, Ahmad Abd-El-Aziz, Leonid Minakhin, Konstantin Severinov, Callum Smits, Alfred A Antson

The assembly of double-stranded DNA bacteriophages is dependent on a small terminase protein that normally plays two important roles. Firstly, the small terminase protein specifically recognizes viral DNA and recruits the large terminase protein, which makes the initial cut in the dsDNA. Secondly, once the complex of the small terminase, the large terminase and the DNA has docked to the portal protein, and DNA translocation into a preformed empty procapsid has begun, the small terminase modulates the ATPase activity of the large terminase. Here, the putative small terminase protein from the thermostable bacteriophage G20C, which infects the Gram-negative eubacterium Thermus thermophilus, has been produced, purified and crystallized. Size-exclusion chromatography-multi-angle laser light scattering data indicate that the protein forms oligomers containing nine subunits. Crystals diffracting to 2.8 Å resolution have been obtained. These belonged to space group P2₁2₁2₁, with unit-cell parameters a = 94.31, b = 125.6, c = 162.8 Å. The self-rotation function and Matthews coefficient calculations are consistent with the presence of a nine-subunit oligomer in the asymmetric unit.

双链DNA噬菌体的组装依赖于一种小的终止酶蛋白,它通常扮演两个重要角色。首先,小终结酶蛋白能特异性地识别病毒 DNA,并招募大终结酶蛋白,由大终结酶蛋白对 dsDNA 进行初始切割。其次,一旦小终结酶、大终结酶和 DNA 的复合物与入口蛋白对接,DNA 开始转运到预先形成的空原囊体中,小终结酶就会调节大终结酶的 ATP 酶活性。本文制备、纯化并结晶了感染革兰氏阴性嗜热菌的恒温噬菌体 G20C 的推定小终结酶蛋白。尺寸排阻色谱-多角度激光光散射数据表明,该蛋白质形成了包含九个亚基的低聚物。晶体衍射分辨率为 2.8 Å。这些晶体属于空间群 P2₁2₁2₁,单胞参数 a = 94.31、b = 125.6、c = 162.8 Å。
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引用次数: 0
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Acta Crystallographica Section F-structural Biology and Crystallization Communications
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