6RUG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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: 10.1039/c9cc05818d
  • Primary Citation of Related Structures:  
    6RUW, 6RUK, 6RUN, 6RUH, 6RUG, 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteinase KA279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WCO (Subject of Investigation/LOI)
Query on WCO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]Co-substituted alpha-Keggin
Co O39 P W11
GUWWRWSAWASHGN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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