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An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.

Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T
Sci Rep 5 14017 (2015)
Related entries: 5d9b, 5d9c

Cited: 25 times
EuropePMC logo PMID: 26360462

Abstract

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection.

Articles - 5d9d mentioned but not cited (1)

  1. An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T. Sci Rep 5 14017 (2015)


Reviews citing this publication (6)

  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. An outlook on using serial femtosecond crystallography in drug discovery. Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. Expert Opin Drug Discov 14 933-945 (2019)
  3. Discerning best practices in XFEL-based biological crystallography - standards for nonstandard experiments. Gorel A, Schlichting I, Barends TRM. IUCrJ 8 532-543 (2021)
  4. Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology. Mizohata E, Nakane T, Fukuda Y, Nango E, Iwata S. Biophys Rev 10 209-218 (2018)
  5. Luciferin-Regenerating Enzyme Crystal Structure Is Solved but its Function Is Still Unclear. Hosseinkhani S, Emamgholi Zadeh E, Sahebazzamani F, Ataei F, Hemmati R. Photochem Photobiol 93 429-435 (2017)
  6. Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins. Hanashima S, Nakane T, Mizohata E. Membranes (Basel) 11 823 (2021)

Articles citing this publication (18)

  1. Recent developments in CrystFEL. White TA, Mariani V, Brehm W, Yefanov O, Barty A, Beyerlein KR, Chervinskii F, Galli L, Gati C, Nakane T, Tolstikova A, Yamashita K, Yoon CH, Diederichs K, Chapman HN. J Appl Crystallogr 49 680-689 (2016)
  2. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Batyuk A, Galli L, Ishchenko A, Han GW, Gati C, Popov PA, Lee MY, Stauch B, White TA, Barty A, Aquila A, Hunter MS, Liang M, Boutet S, Pu M, Liu ZJ, Nelson G, James D, Li C, Zhao Y, Spence JC, Liu W, Fromme P, Katritch V, Weierstall U, Stevens RC, Cherezov V. Sci Adv 2 e1600292 (2016)
  3. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. Nature 539 43-47 (2016)
  4. Hydroxyethyl cellulose matrix applied to serial crystallography. Sugahara M, Nakane T, Masuda T, Suzuki M, Inoue S, Song C, Tanaka R, Nakatsu T, Mizohata E, Yumoto F, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Numata K, Nango E, Iwata S. Sci Rep 7 703 (2017)
  5. Short-wavelength free-electron laser sources and science: a review. Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Rep Prog Phys 80 115901 (2017)
  6. Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent. Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E. Proc Natl Acad Sci U S A 113 13039-13044 (2016)
  7. Advances in long-wavelength native phasing at X-ray free-electron lasers. Nass K, Cheng R, Vera L, Mozzanica A, Redford S, Ozerov D, Basu S, James D, Knopp G, Cirelli C, Martiel I, Casadei C, Weinert T, Nogly P, Skopintsev P, Usov I, Leonarski F, Geng T, Rappas M, Doré AS, Cooke R, Nasrollahi Shirazi S, Dworkowski F, Sharpe M, Olieric N, Bacellar C, Bohinc R, Steinmetz MO, Schertler G, Abela R, Patthey L, Schmitt B, Hennig M, Standfuss J, Wang M, Milne CJ. IUCrJ 7 965-975 (2020)
  8. Oil-free hyaluronic acid matrix for serial femtosecond crystallography. Sugahara M, Song C, Suzuki M, Masuda T, Inoue S, Nakane T, Yumoto F, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Numata K, Iwata S. Sci Rep 6 24484 (2016)
  9. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundström U, Koglin JE, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM, Boutet S. Nat Commun 7 13388 (2016)
  10. Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability. Gorel A, Motomura K, Fukuzawa H, Doak RB, Grünbein ML, Hilpert M, Inoue I, Kloos M, Kovácsová G, Nango E, Nass K, Roome CM, Shoeman RL, Tanaka R, Tono K, Joti Y, Yabashi M, Iwata S, Foucar L, Ueda K, Barends TRM, Schlichting I. Nat Commun 8 1170 (2017)
  11. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. IUCrJ 8 905-920 (2021)
  12. 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)
  13. Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed β-propeller hydrolase family. Pääkkönen J, Hakulinen N, Andberg M, Koivula A, Rouvinen J. Protein Sci 31 371-383 (2022)
  14. Xylonolactonase from Caulobacter crescentus Is a Mononuclear Nonheme Iron Hydrolase. Pääkkönen J, Penttinen L, Andberg M, Koivula A, Hakulinen N, Rouvinen J, Jänis J. Biochemistry 60 3046-3049 (2021)
  15. Luciferin Regeneration in Firefly Bioluminescence via Proton-Transfer-Facilitated Hydrolysis, Condensation and Chiral Inversion. Cheng YY, Liu YJ. Chemphyschem 20 1719-1727 (2019)
  16. Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX. Pan D, Oyama R, Sato T, Nakane T, Mizunuma R, Matsuoka K, Joti Y, Tono K, Nango E, Iwata S, Nakatsu T, Kato H. IUCrJ 9 134-145 (2022)
  17. Effect of impurities and post-experimental purification in SAD phasing with serial femtosecond crystallography data. Zhang T, Gu Y, Fan H. Acta Crystallogr D Struct Biol 72 789-794 (2016)
  18. Single-support serial isomorphous replacement phasing. Foos N, Rizk M, Nanao MH. Acta Crystallogr D Struct Biol 78 716-724 (2022)


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