Evidence map›Paper›PMID 28361898›Full record

ArticleScientific reports2017

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

Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Takanori Nakane, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima and 7 more

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
2.0field-weighted citation impact, top 14% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 38 citations in OpenAlex.

  1. Article
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  11. Isoprenoid-chained lipid EROCOCScientific reports · 2020
    Article
  12. Article
  13. High-resolution crystal structures of a "half sandwich"-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2020
    Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Synthesis of silver nanoparticles byJournal, genetic engineering & biotechnology · 2018
    Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 7 institutions in 2 countries.

Tetsuya MasudaDivision of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Mamoru SuzukiRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Shigeyuki InoueRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Changyong SongRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Takanori NakaneDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Eriko NangoRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Rie TanakaRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Kensuke TonoJapan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Yasumasa JotiJapan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Takashi KameshimaJapan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Takaki HatsuiRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Makina YabashiRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Bunzo MikamiDivision of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Keiji NumataEnzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan.
So IwataRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Michihiro SugaharaRIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
SPring-8 · JPJapan Synchrotron Radiation Research Institute · JPKyoto University · JPThe University of Tokyo · JPOsaka University · JPPohang University of Science and Technology · KRRIKEN Center for Sustainable Resource Science · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Catalytic DomainCrystallography, X-RayEndopeptidase KSerine EndopeptidasesSerine ProteasesSynchrotronsTemperatureEndopeptidase KSerine EndopeptidasesSerine Proteases

Identifiers

PMID28361898
PMCPMC5374539
OpenAlexW2600775259

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.