3Q5G | pdb_00003q5g

Sulphur SAD structure solution of proteinase K grown in SO4 solution

• PDB DOI: https://doi.org/10.2210/pdb3Q5G/pdb

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


• Deposited: 2010-12-28 Released: 2011-06-29 
• Deposition Author(s): Jakoncic, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.167 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.126 (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: 29.19 kDa 
• Atom Count: 2,521 
• 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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.167 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.864	α = 90
b = 67.864	β = 90
c = 102.193	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: 2011-06-29 
Deposition Author(s): Jakoncic, J.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary