6J43 | pdb_00006j43

Proteinase K determined by PAL-XFEL

• PDB DOI: https://doi.org/10.2210/pdb6J43/pdb

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


• Deposited: 2019-01-07 Released: 2020-01-15 
• Deposition Author(s): Lee, S.J., Park, J.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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

• PubMed: 32280322 
• DOI: https://doi.org/10.1107/S1600576720002423
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Mechanical Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea.
PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea.
College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seoul, 02841, Republic of Korea.
Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seoul, 02841, Republic of Korea.
Department of Materials Science and Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea.
Department of Life Sciences, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 2,261 
• 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  Gene Names: PROK EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.54	α = 90
b = 68.54	β = 90
c = 108.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Lee, S.J., Park, J.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029733
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016R1C1B2014609
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1D1A1B03028119

Revision History  

• 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