2ID8 | pdb_00002id8

Crystal structure of Proteinase K

• PDB DOI: https://doi.org/10.2210/pdb2ID8/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Mutation(s): Yes 


• Deposited: 2006-09-14 Released: 2006-10-10 
• Deposition Author(s): Wang, J., Dauter, M., Dauter, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.159 (Depositor) 
• R-Value Work: 
  0.133 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Literature

What can be done with a good crystal and an accurate beamline?

Wang, J., Dauter, M., Dauter, Z.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1475-1483

• PubMed: 17139083 
• DOI: https://doi.org/10.1107/S0907444906038534
• Primary Citation Related Structures: 
  2ID8


• PubMed Abstract: 
  

  X-ray single-wavelength anomalous diffraction (SAD) data from a crystal of proteinase K were collected using synchrotron radiation of 0.98 A wavelength at SER-CAT 22-ID beamline, Advanced Photon Source, Argonne National Laboratory. At this wavelength, the expected Bijvoet ratio resulting from the presence of one calcium, one chloride and ten S atoms in the 279-residue protein is extremely small at approximately 0.46%. The direct-methods program SHELXD located 11 anomalous sites using data truncated to 2 A resolution. SHELXE was used to produce an easily interpretable electron-density map. This study shows that an accurate beamline and a good-quality crystal provide the possibility of successfully using a very weak anomalous signal of sulfur measured at a short wavelength for phasing a protein structure, even if a small degree of radiation damage is present.

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Organizational Affiliation: 
• SAIC-Frederick Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA.

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: 2,332 
• 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): 1  EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2DB	G [auth A]	(S)-(2,3-DIHYDROXYPROPOXY)TRIHYDROXYBORATE C3 H10 B O6 KLKDDPLTQSQDLA-VKHMYHEASA-N
NO3	C [auth A], D [auth A], E [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.159 (Depositor) 
• R-Value Work:  0.133 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.55	α = 90
b = 67.55	β = 90
c = 106.88	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Wang, J., Dauter, M., Dauter, Z.

Revision History  

• Version 1.0: 2006-10-10
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary