6IG6

Crystal structure of lysozyme delivered in polyacrylamide using x-ray free electron laser

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Expression System: Gallus gallus

  • Deposited: 2018-09-25 Released: 2018-11-07 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (Korea) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Polyacrylamide injection matrix for serial femtosecond crystallography.

Park, J.Park, S.Kim, J.Park, G.Cho, Y.Nam, K.H.

(2019) Sci Rep 9: 2525-2525

  • DOI: 10.1038/s41598-019-39020-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the ...

    Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.


    Organizational Affiliation

    Sprint Bioscience , 141 57 Huddinge , Sweden.,School of Chemistry and Biochemistry , The University of Western Australia (M313) , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Infectious Diseases Discovery , GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.,Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045.,Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Medicines Discovery Institute , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom.,Division of Biotechnology, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea. jaehyun.park@postech.ac.kr.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Polgenix Inc., Cleveland, OH 44106, USA.,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Department of Life Science, POSTECH, Pohang, Gyeongbuk, Republic of Korea.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,York Structural Biology Laboratory , Department of Chemistry , The University of York , YO10 5DD , UK.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,VA Tennessee Valley Healthcare System , 1310 24th Avenue S. , Nashville , Tennessee 37212 , United States.,University of Puerto Rico at Humacao, Humacao, PR, USA.,Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada . Email: dvocadlo@sfu.ca.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.600α = 90.00
b = 79.600β = 90.00
c = 38.200γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata scaling
CrystFELdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-25 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9F6029736

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection
  • Version 1.2: 2019-05-22
    Type: Data collection, Database references
  • Version 1.3: 2019-08-28
    Type: Data collection
  • Version 1.4: 2019-09-18
    Type: Data collection