Co-substituted alpha-Keggin bound to Proteinase K solved by MR

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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Transition metal-substituted Keggin polyoxotungstates enabling covalent attachment to proteinase K upon co-crystallization.

Breibeck, J.Bijelic, A.Rompel, A.

(2019) Chem Commun (Camb) 55: 11519-11522

  • DOI: https://doi.org/10.1039/c9cc05818d
  • Primary Citation of Related Structures:  
    6RUG, 6RUH, 6RUK, 6RUN, 6RUW, 6RVE, 6RVG

  • PubMed Abstract: 

    The use of α- and β-Keggin polyoxotungstates (POTs) substituted by a single first row transition metal ion (CoII, NiII, CuII, ZnII) as superchaotropic crystallization additives led to covalent and non-covalent interactions with protein side-chains of proteinase K. Two major Keggin POT binding sites in proteinase K were identified, both stabilizing the orientation of the substituted metal site towards the protein surface and suggesting increased protein affinity for the substitution sites. The formation of all observed covalent bonds involves the same aspartate carboxylate, taking the role of a terminal oxygen with the Keggin α-isomer or even, in an unprecedented scenario, a bridging cluster oxygen with the β-isomer. Covalent bond formation with the protein carboxylate was observed only with the NiII- and CoII-substituted POTs, following the HSAB concept and the principle of metal immobilization.

  • Organizational Affiliation

    Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria. annette.rompel@univie.ac.at.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.86α = 90
b = 67.86β = 90
c = 102.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP27534

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description