3AJ9

X-ray analysis of Crystal of Proteinase K Obtained from D2O Solution Using PEG 8000


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K

Chatake, T.Ishikawa, T.Yanagisawa, Y.Yamada, T.Tanaka, I.Fujiwara, S.Morimoro, Y.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1334-1338

  • DOI: https://doi.org/10.1107/S1744309111031903
  • Primary Citation of Related Structures:  
    3AJ8, 3AJ9

  • PubMed Abstract: 

    Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.


  • Organizational Affiliation

    Research Reactor Institute, Kyoto University, Ashashironishi 2, Kumatori, Osaka, Japan. chatake@rri.kyoto-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.1α = 90
b = 68.1β = 90
c = 102.464γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Database references
  • Version 1.3: 2012-05-02
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary