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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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Crystallization and preliminary X-ray study of the deaminase AmnE from Pseudomonas sp. AP-3. Corrigendum","authors":"Dan Yu, Yongji Jiang, Jianfeng Hou, Shuai Chen, Guofang Zhang, Xiang Liu, Hui Dong, Bo Yu","doi":"10.1107/S1744309113029321","DOIUrl":"https://doi.org/10.1107/S1744309113029321","url":null,"abstract":"A correction is made to the article by Yu et al. (2013). Acta Cryst. F69, 812–814.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"17 1","pages":"1314 - 1314"},"PeriodicalIF":0.9,"publicationDate":"2013-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90952374","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}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Crystallization and preliminary X-ray study of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4. Corrigendum","authors":"Hui Dong, Shujing Xu, Xiaoyu Lu, Guangzheng He, Ranran Zhao, Shuai Chen, Sheng Fu, J. Ju","doi":"10.1107/S1744309113029114","DOIUrl":"https://doi.org/10.1107/S1744309113029114","url":null,"abstract":"A correction is made to the article by Dong et al. (2013). Acta Cryst. F69, 660–662.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"23 1","pages":"1310 - 1310"},"PeriodicalIF":0.9,"publicationDate":"2013-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85008083","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}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-10-31 DOI: 10.1107/S1744309113029126
P. Nogly, Rute Castro, Matteo de Rosa, A. R. Neves, Helena Santos, Margarida Archer
{"title":"Production and crystallization of α-phosphoglucomutase from Lactococcus lactis. Corrigendum","authors":"P. Nogly, Rute Castro, Matteo de Rosa, A. R. Neves, Helena Santos, Margarida Archer","doi":"10.1107/S1744309113029126","DOIUrl":"https://doi.org/10.1107/S1744309113029126","url":null,"abstract":"A correction is made to the article by Nogly et al. (2012). Acta Cryst. F68, 1113–1115.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"23 1","pages":"1313 - 1313"},"PeriodicalIF":0.9,"publicationDate":"2013-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78976174","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}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Identification, characterization and preliminary X-ray diffraction analysis of the rolling-circle replication initiator protein from plasmid pSTK1.","authors":"Stephen B Carr, Lauren B Mecia, Simon E V Phillips, Christopher D Thomas","doi":"10.1107/S1744309113023828","DOIUrl":"10.1107/S1744309113023828","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 10","pages":"1123-6"},"PeriodicalIF":0.9,"publicationDate":"2013-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9712153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.","authors":"Richard N A Martin, John E McGeehan, Neil J Ball, Simon D Streeter, Sarah-Jane Thresh, G G Kneale","doi":"10.1107/S174430911302126X","DOIUrl":"10.1107/S174430911302126X","url":null,"abstract":"<p><p>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. </p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 9","pages":"962-6"},"PeriodicalIF":0.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31694337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser.","authors":"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","doi":"10.1107/S174430911302099X","DOIUrl":"10.1107/S174430911302099X","url":null,"abstract":"<p><p>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. </p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 9","pages":"1066-9"},"PeriodicalIF":0.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31693553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-09-01 Epub Date: 2013-08-19 DOI: 10.1107/S1744309113020289
Avinash S Punekar, Maria Selmer
{"title":"Purification, crystallization and preliminary X-ray diffraction analysis of the 23S rRNA methyltransferase RlmJ from Escherichia coli.","authors":"Avinash S Punekar, Maria Selmer","doi":"10.1107/S1744309113020289","DOIUrl":"10.1107/S1744309113020289","url":null,"abstract":"<p><p>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).</p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 9","pages":"1001-3"},"PeriodicalIF":0.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31693722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-08-19 DOI: 10.1107/S1744309113012001
P. Harris, K. Raghunathan, R. Spurbeck, C. Arvidson, D. Arvidson
{"title":"Expression, purification, crystallization and preliminary X-ray studies of Lactobacillus jensenii enolase. Corrigendum","authors":"P. Harris, K. Raghunathan, R. Spurbeck, C. Arvidson, D. Arvidson","doi":"10.1107/S1744309113012001","DOIUrl":"https://doi.org/10.1107/S1744309113012001","url":null,"abstract":"A correction is made to the article by Harris et al. [(2010) Acta Cryst. F66, 938–940].","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"59 1","pages":"1070 - 1070"},"PeriodicalIF":0.9,"publicationDate":"2013-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74381736","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}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium.","authors":"N Azim, E Deery, M J Warren, P Erskine, J B Cooper, S P Wood, M Akhtar","doi":"10.1107/S1744309113018526","DOIUrl":"10.1107/S1744309113018526","url":null,"abstract":"<p><p>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. </p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 8","pages":"906-8"},"PeriodicalIF":0.9,"publicationDate":"2013-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31626549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Acta Crystallographica Section F-structural Biology and Crystallization Communications 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
{"title":"The putative small terminase from the thermophilic dsDNA bacteriophage G20C is a nine-subunit oligomer.","authors":"Juan Loredo-Varela, Maria Chechik, Vladimir M Levdikov, Ahmad Abd-El-Aziz, Leonid Minakhin, Konstantin Severinov, Callum Smits, Alfred A Antson","doi":"10.1107/S1744309113017016","DOIUrl":"10.1107/S1744309113017016","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 8","pages":"876-9"},"PeriodicalIF":0.9,"publicationDate":"2013-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31626085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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