6K2V | pdb_00006k2v

Crystal structure of proteinase K from Engyodontium album


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Viscosity-adjustable grease matrices for serial nanocrystallography.

Sugahara, M.Motomura, K.Suzuki, M.Masuda, T.Joti, Y.Numata, K.Tono, K.Yabashi, M.Ishikawa, T.

(2020) Sci Rep 10: 1371-1371

  • DOI: https://doi.org/10.1038/s41598-020-57675-7
  • Primary Citation of Related Structures:  
    6K2P, 6K2R, 6K2S, 6K2T, 6K2V, 6K2W, 6K2X

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) has enabled determination of room temperature structures of proteins with minimum radiation damage. A highly viscous grease matrix acting as a crystal carrier for serial sample loading at a low flow rate of ~0.5 μl min -1 was introduced into the beam path of X-ray free-electron laser. This matrix makes it possible to determine the protein structure with a sample consumption of less than 1 mg of the protein. The viscosity of the matrix is an important factor in maintaining a continuous and stable sample column from a nozzle of a high viscosity micro-extrusion injector for serial sample loading. Using conventional commercial grease (an oil-based, viscous agent) with insufficient control of viscosity in a matrix often gives an unexpectedly low viscosity, providing an unstable sample stream, with effects such as curling of the stream. Adjustment of the grease viscosity is extremely difficult since the commercial grease contains unknown compounds, which may act as unexpected inhibitors of proteins. This study introduces two novel grease matrix carriers comprising known compounds with a viscosity higher than that of conventional greases, to determine the proteinase K structure from nano-/microcrystals.


  • Organizational Affiliation

    RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan. msuga@spring8.or.jp.


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: 1.60 Å
  • R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.28α = 90
b = 68.28β = 90
c = 108.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
CrystFELdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-11-13
    Changes: Structure summary
  • Version 1.3: 2025-03-05
    Changes: Database references