title: Atomic resolution structure of serine protease proteinase K at ambient temperature.
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.
authors.affiliation: Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.|RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Masuda
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.|Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Mamoru
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.|Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Inoue
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.|Department of Physics, POSTECH, Pohang 790-784, Korea.
authors.forename: Changyong
authors.initials: C
authors.lastname: Song
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Nakane
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Eriko
authors.initials: E
authors.lastname: Nango
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Rie
authors.initials: R
authors.lastname: Tanaka
authors.affiliation: Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Tono
authors.affiliation: Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Joti
authors.affiliation: Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kameshima
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Takaki
authors.initials: T
authors.lastname: Hatsui
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Makina
authors.initials: M
authors.lastname: Yabashi
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
authors.forename: Bunzo
authors.initials: B
authors.lastname: Mikami
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.affiliation: Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Keiji
authors.initials: K
authors.lastname: Numata
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.|Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: So
authors.initials: S
authors.lastname: Iwata
authors.affiliation: RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Michihiro
authors.initials: M
authors.lastname: Sugahara
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray / Q000379:methods; D019286:Endopeptidase K / Q000737:chemistry*; D012697:Serine Endopeptidases / Q000737:chemistry*; D057057:Serine Proteases / Q000737:chemistry*; D017356:Synchrotrons; D013696:Temperature
chemical_list: D057057:Serine Proteases; D012697:Serine Endopeptidases; D019286:Endopeptidase K