8RSF | pdb_00008rsf

Proteinase K measured via serial crystallography from a kapton HARE-chip (50 micron)

• PDB DOI: https://doi.org/10.2210/pdb8RSF/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Mutation(s): No 


• Deposited: 2024-01-24 Released: 2024-12-04 
• Deposition Author(s): Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., Sung, S., von Stetten, D., Mehrabi, P., Schulz, E.C.
• Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Economic Affairs and Energy

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Kapton-based HARE chips for fixed-target serial crystallography

Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., Sung, S., von Stetten, D., Mehrabi, P., Blatter, G., Lu, G., Bernhard, S., Osbild, M., Schulz, E.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.47 kDa 
• Atom Count: 2,332 
• Modeled Residue Count: 279 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	384	Parengyodontium album	Mutation(s): 0  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	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.5	α = 90
b = 68.5	β = 90
c = 108.75	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: 2024-12-04 
Deposition Author(s): Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., Sung, S., von Stetten, D., Mehrabi, P., Schulz, E.C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	458246365
German Research Foundation (DFG)	Germany	451079909
German Federal Ministry for Economic Affairs and Energy	Germany	01KI2114

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release