2PYZ | pdb_00002pyz

Crystal structure of the complex of proteinase K with auramine at 1.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PYZ/pdb

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


• Deposited: 2007-05-17 Released: 2007-07-03 
• Deposition Author(s): Singh, A.K., Singh, N., Sinha, M., Sharma, S., Bhushan, A., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.156 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of Proteinase K with auramine at 1.8A resolution

Singh, A.K., Singh, N., Sinha, M., Sharma, S., Bhushan, A., Kaur, P., Singh, T.P.

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: 29.37 kDa 
• Atom Count: 2,387 
• 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  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
AU4	E [auth A]	4,4'-(AMINOMETHYLENE)BIS(N,N-DIMETHYLANILINE) C17 H23 N3 SGTJPINAQYDQHG-UHFFFAOYSA-N
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: 1.79 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.156 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.299	α = 90
b = 68.299	β = 90
c = 108.379	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Singh, A.K., Singh, N., Sinha, M., Sharma, S., Bhushan, A., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary