6RUH

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

• PDB DOI: https://doi.org/10.2210/pdb6RUH/pdb

• Classification: PROTEIN BINDING
• Organism(s): Parengyodontium album
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2019-09-18 
• Deposition Author(s): Breibeck, J., Bijelic, A., Rompel, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.158 
• R-Value Work: 0.147 
• R-Value Observed: 0.147 

Starting Model: experimental

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

• PubMed: 31490500 
• 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.

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Organizational Affiliation: 

Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,506 
• Modelled 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): 0  EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WNI	B [auth A], C [auth A]	Ni-substituted alpha-Keggin Ni O39 P W11 FYPBVTPREGHXRM-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.158 
• R-Value Work: 0.147 
• R-Value Observed: 0.147 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.96	α = 90
b = 67.96	β = 90
c = 102.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Breibeck, J., Bijelic, A., Rompel, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P27534

Revision History  

• 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
• Version 1.3: 2024-11-13
  Changes: Structure summary