3QMP | pdb_00003qmp

Selenium SAD structure solution of proteinase K grown in SO4-less solution and soaked in selenate.

• PDB DOI: https://doi.org/10.2210/pdb3QMP/pdb

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


• Deposited: 2011-02-04 Released: 2012-01-18 
• Deposition Author(s): Jakoncic, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.119 (Depositor), 0.118 (DCC) 
• R-Value Work: 
  0.103 (Depositor), 0.104 (DCC) 
• R-Value Observed: 
  0.104 (Depositor) 

Literature

Crystallization of macromolecules in selenate to solve the phase problem

Jakoncic, J.

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: 29.35 kDa 
• Atom Count: 2,757 
• Modelled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SE4	D [auth A]	SELENATE ION O4 Se QYHFIVBSNOWOCQ-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.119 (Depositor), 0.118 (DCC) 
• R-Value Work:  0.103 (Depositor), 0.104 (DCC) 
• R-Value Observed: 0.104 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.967	α = 90
b = 67.967	β = 90
c = 102.215	γ = 90

Software Package:

Software Name	Purpose
DCS_X6A	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Jakoncic, J.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary