6J43

Proteinase K determined by PAL-XFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography.

Lee, D.Park, S.Lee, K.Kim, J.Park, G.Nam, K.H.Baek, S.Chung, W.K.Lee, J.L.Cho, Y.Park, J.

(2020) J Appl Crystallogr 53: 477-485

  • DOI: https://doi.org/10.1107/S1600576720002423
  • Primary Citation of Related Structures:  
    6J43

  • PubMed Abstract: 

    Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.


  • Organizational Affiliation

    Department of Mechanical Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea.


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: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.54α = 90
b = 68.54β = 90
c = 108.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9F6029733
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1C1B2014609
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1D1A1B03028119

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references, Derived calculations
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary