2V8B | pdb_00002v8b

SAD Structure solution of Proteinase K grown in selenate solution

• PDB DOI: https://doi.org/10.2210/pdb2V8B/pdb

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


• Deposited: 2007-08-06 Released: 2008-08-26 
• Deposition Author(s): Jakoncic, J., Stojanoff, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 
  0.103 (Depositor) 
• R-Value Work: 
  0.090 (Depositor) 
• R-Value Observed: 
  0.091 (Depositor) 

Literature

Selenate Substitution: Application in Protein Crystallography

Jakoncic, J., Stojanoff, V.

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: 29.14 kDa 
• Atom Count: 2,754 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SE4	C [auth A]	SELENATE ION O4 Se QYHFIVBSNOWOCQ-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free:  0.103 (Depositor) 
• R-Value Work:  0.090 (Depositor) 
• R-Value Observed: 0.091 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.053	α = 90
b = 68.053	β = 90
c = 102.553	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Jakoncic, J., Stojanoff, V.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Data collection, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary