5KXV

Structure Proteinase K at 0.98 Angstroms

• PDB DOI: https://doi.org/10.2210/pdb5KXV/pdb

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


• Deposited: 2016-07-20 Released: 2017-06-07 
• Deposition Author(s): Masuda, T., Suzuki, M., Inoue, S., Numata, K., Sugahara, M.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.114 
• R-Value Work: 0.100 
• R-Value Observed: 0.101 

Starting Model: experimental

Literature

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

Masuda, T., Suzuki, M., Inoue, S., Song, C., Nakane, T., Nango, E., Tanaka, R., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Mikami, B., Nureki, O., Numata, K., Iwata, S., Sugahara, M.

(2017) Sci Rep 7: 45604-45604

• PubMed: 28361898 
• DOI: https://doi.org/10.1038/srep45604
• Primary Citation of Related Structures:  
  5KXU, 5KXV


• PubMed 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.

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Organizational Affiliation: 

Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.29 kDa 
• Atom Count: 2,831 
• Modelled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 1  EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.114 
• R-Value Work: 0.100 
• R-Value Observed: 0.101 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.577	α = 90
b = 67.577	β = 90
c = 107.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Masuda, T., Suzuki, M., Inoue, S., Numata, K., Sugahara, M.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	25650026

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2021-10-27
  Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary