5B1D | pdb_00005b1d

Crystal structure of proteinase K from Engyodontium album

• PDB DOI: https://doi.org/10.2210/pdb5B1D/pdb

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


• Deposited: 2015-12-03 Released: 2016-12-14 
• Deposition Author(s): Sugahara, M., Suzuki, M., Numata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.183 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Literature

Crystal structure of proteinase K from Engyodontium album

Sugahara, M., Suzuki, M., Numata, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 2,104 
• 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): 0  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: 2.30 Å
• R-Value Free:  0.183 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1249397

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.8	α = 90
b = 68.8	β = 90
c = 109.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Sugahara, M., Suzuki, M., Numata, K.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary