5kxv › Citations

Atomic resolution structure of serine protease proteinase K at ambient temperature.

<div class='caption-title'>Stereo views of hydrogen atoms in secondary elements in SFX structure.</div>
<div class='caption-title'>Electron density maps around catalytic triad and oxyanion hole in SFX structure.</div>
<div class='caption-title'>Comparison of SFX and SRX structures in the active site.</div>
Masuda T, Suzuki M, Inoue S, Song C, Nakane T, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Mikami B, Nureki O, Numata K, Iwata S, Sugahara M
OpenAccess logo Sci Rep 7 45604 (2017)
Cited: 14 times
EuropePMC logo PMID: 28361898

Abstract

Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.

Articles - 5kxv mentioned but not cited (3)

  1. Atomic resolution structure of serine protease proteinase K at ambient temperature. Masuda T, Suzuki M, Inoue S, Song C, Nakane T, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Mikami B, Nureki O, Numata K, Iwata S, Sugahara M. Sci Rep 7 45604 (2017)
  2. 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. Tolstikova A, Levantino M, Yefanov O, Hennicke V, Fischer P, Meyer J, Mozzanica A, Redford S, Crosas E, Opara NL, Barthelmess M, Lieske J, Oberthuer D, Wator E, Mohacsi I, Wulff M, Schmitt B, Chapman HN, Meents A. IUCrJ 6 927-937 (2019)
  3. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (3)

  1. A Bright Future for Serial Femtosecond Crystallography with XFELs. Johansson LC, Stauch B, Ishchenko A, Cherezov V. Trends Biochem Sci 42 749-762 (2017)
  2. Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM. Ishchenko A, Gati C, Cherezov V. Curr Opin Struct Biol 51 44-52 (2018)
  3. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Khakurel KP, Angelov B, Andreasson J. Molecules 24 E3490 (2019)

Articles citing this publication (8)

  1. Ab initio phasing macromolecular structures using electron-counted MicroED data. Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Nat Methods 19 724-729 (2022)
  2. Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography. Lee D, Park S, Lee K, Kim J, Park G, Nam KH, Baek S, Chung WK, Lee JL, Cho Y, Park J. J Appl Crystallogr 53 477-485 (2020)
  3. Synthesis of silver nanoparticles by Bacillus clausii and computational profiling of nitrate reductase enzyme involved in production. Mukherjee K, Gupta R, Kumar G, Kumari S, Biswas S, Padmanabhan P. J Genet Eng Biotechnol 16 527-536 (2018)
  4. Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography. Ihara K, Hato M, Nakane T, Yamashita K, Kimura-Someya T, Hosaka T, Ishizuka-Katsura Y, Tanaka R, Tanaka T, Sugahara M, Hirata K, Yamamoto M, Nureki O, Tono K, Nango E, Iwata S, Shirouzu M. Sci Rep 10 19305 (2020)
  5. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. Nat Commun 14 1086 (2023)
  6. Viscosity-adjustable grease matrices for serial nanocrystallography. Sugahara M, Motomura K, Suzuki M, Masuda T, Joti Y, Numata K, Tono K, Yabashi M, Ishikawa T. Sci Rep 10 1371 (2020)
  7. Serial macromolecular crystallography at ALBA Synchrotron Light Source. Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. J Synchrotron Radiat 29 896-907 (2022)
  8. Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography. Takaba K, Maki-Yonekura S, Inoue I, Tono K, Hamaguchi T, Kawakami K, Naitow H, Ishikawa T, Yabashi M, Yonekura K. Nat Chem 15 491-497 (2023)


Quick links