7A9F | pdb_00007a9f

Co-substituted Keggin silicotungstate with covalent bond to proteinase K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.174 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Literature

Speciation of Transition-Metal-Substituted Keggin-Type Silicotungstates Affected by the Co-crystallization Conditions with Proteinase K.

Breibeck, J.Tanuhadi, E.Gumerova, N.I.Giester, G.Prado-Roller, A.Rompel, A.

(2021) Inorg Chem 60: 15096-15100

  • DOI: https://doi.org/10.1021/acs.inorgchem.1c02005
  • Primary Citation of Related Structures:  
    7A9F, 7A9K, 7A9M

  • PubMed Abstract: 

    We report on the synthesis of the tetrasubstituted sandwich-type Keggin silicotungstates as the pure Na salts Na 14 [(A-α-SiW 10 O 37 ) 2 {Co 4 (OH) 2 (H 2 O) 2 }]·37H 2 O ( Na{SiW 10 Co 2 } 2 ) and Na 14 [(A-α-SiW 10 O 37 ) 2 {Ni 4 (OH) 2 (H 2 O) 2 }]·77.5H 2 O ( Na{SiW 10 Ni 2 } 2 ), which were prepared by applying a new synthesis protocol and characterized thoroughly in the solid state by single-crystal and powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis, and elemental analysis. Proteinase K was applied as a model protein and the polyoxotungstate (POT)-protein interactions of Na{SiW 10 Co 2 } 2 and Na{SiW 10 Ni 2 } 2 were studied side by side with the literature-known K 5 Na 3 [A-α-SiW 9 O 34 (OH) 3 {Co 4 (OAc) 3 }]·28.5H 2 O ( {SiW 9 Co 4 } ) featuring the same number of transition metals. Testing the solution behavior of applied POTs under the crystallization conditions (sodium acetate buffer, pH 5.5) by time-dependent UV/vis spectroscopy and electrospray ionization mass spectrometry speciation studies revealed an initial dissociation of the sandwich POTs to the disubstituted Keggin anions H x Na 5- x [SiW 10 Co 2 O 38 ] 3- and H x Na 5- x [SiW 10 Ni 2 O 38 ] 3- ( {SiW 10 M 2 } , M = Co II and Ni II ) followed by partial rearrangement to the monosubstituted compounds ( α-{SiW 11 Co} and α-{SiW 11 Ni} ) after 1 week of aging. The protein crystal structure analysis revealed monosubstituted α-Keggin POTs in two conserved binding positions for all three investigated compounds, with one of these positions featuring a covalent attachment of the POT anion to an aspartate carboxylate. Despite the presence of both mono- and disubstituted anions in a crystallization mixture, proteinase K selectively binds to monosubstituted anions because of their preferred charge density for POT-protein interaction.


  • Organizational Affiliation

    Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria.


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: 1.62 Å
  • R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.11α = 90
b = 68.11β = 90
c = 102.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted R5QClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP27534

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary