5MJL

Single-shot pink beam serial crystallography: Proteinase K

  • Classification: HYDROLASE
  • Organism(s): Parengyodontium album
  • Expression System: Parengyodontium album
  • Mutation(s): Yes 

  • Deposited: 2016-12-01 Released: 2017-11-15 
  • Deposition Author(s): Meents, A., Oberthuer, D., Lieske, J., Srajer, V.
  • Funding Organization(s): European Cluster of Advanced Laser Light Sources (EUCALL), Virtual Institute, Helmholtz Association, Advanced Photon Source, a U.S. Department of Energy (DOE), Argonne National Laboratory, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Philip Anfinrud (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Pink-beam serial crystallography.

Meents, A.Wiedorn, M.O.Srajer, V.Henning, R.Sarrou, I.Bergtholdt, J.Barthelmess, M.Reinke, P.Y.A.Dierksmeyer, D.Tolstikova, A.Schaible, S.Messerschmidt, M.Ogata, C.M.Kissick, D.J.Taft, M.H.Manstein, D.J.Lieske, J.Oberthuer, D.Fischetti, R.F.Chapman, H.N.

(2017) Nat Commun 8: 1281-1281

  • DOI: https://doi.org/10.1038/s41467-017-01417-3
  • Primary Citation of Related Structures:  
    5MJL, 5MJM, 5MJP, 5MJQ, 5O7M

  • PubMed Abstract: 

    Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.


  • Organizational Affiliation

    Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany. alke.meents@desy.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 1 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 68.3β = 90
c = 108.3γ = 90
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
Precognition/Epinorm (RenzResearch)data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Cluster of Advanced Laser Light Sources (EUCALL)--
Virtual Institute, Helmholtz AssociationVH-VI-403
Advanced Photon Source, a U.S. Department of Energy (DOE), Argonne National LaboratoryDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM111072
Philip Anfinrud (NIH/NIDDK)NSF award 1231306

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary