5KXU | pdb_00005kxu

Structure Proteinase K determined by SACLA

• PDB DOI: https://doi.org/10.2210/pdb5KXU/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: 1.20 Å
• R-Value Free: 
  0.129 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

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 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.
RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.
Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Department of Physics, POSTECH, Pohang 790-784, Korea.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.1 kDa 
• Atom Count: 2,528 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.129 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1350027

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.5	α = 90
b = 68.5	β = 90
c = 108.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling

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: 2018-01-24
  Changes: Data collection
• Version 1.2: 2021-10-27
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-08
  Changes: Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary