6QSG | pdb_00006qsg

Crystal structure of the hybrid bioinorganic complex of Pizza6S and Keggin (STA)

• PDB DOI: https://doi.org/10.2210/pdb6QSG/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-20 Released: 2020-03-18 
• Deposition Author(s): Noguchi, H., Vandebroek, L., Kamata, K., Tame, J.R.H., Van Meervelt, L., Parac-Vogt, T.N., Voet, A.R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.186 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry.

Vandebroek, L., Noguchi, H., Kamata, K., Tame, J.R.H., Van Meervelt, L., Parac-Vogt, T.N., Voet, A.R.D.

(2020) Chem Commun (Camb) 56: 11601-11604

• PubMed: 32869783 
• DOI: https://doi.org/10.1039/d0cc05071g
• Primary Citation Related Structures: 
  6QSD, 6QSE, 6QSF, 6QSG, 6QSH


• PubMed Abstract: 
  

  Novel bioinorganic hybrid materials based on proteins and inorganic clusters have enormous potential for the development of hybrid catalysts that synergistically combine properties of both materials. Here we report the creation of hybrid assemblies between a computationally designed symmetrical protein Pizza6-S and different polyoxometalates with matching symmetry: the tellurotungstic Anderson-Evans (Na6[TeW6O24]·22H2O) (TEW); Keggin (H4[SiW12O40]·6H2O) (STA); and 1 : 2 CeIII-substituted Keggin (K11[CeIII[PW11O39]2]·20H2O) (Ce-K). This results in the formation of complexes with clearly defined stoichiometries in solution. Crystal structures validate the complexes as building blocks for the formation of larger assemblies.

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Organizational Affiliation: 
• Laboratory for Bioinorganic Chemistry, KU Leuven Department of Chemistry, Celestijnenlaan 200F, 3001 Leuven, Belgium and Biomolecular Architecture, KU Leuven Department of Chemistry, Celestijnenlaan 200F, 3001 Leuven, Belgium.
Laboratory for Biomolecular Modelling and Design, KU Leuven Department of Chemistry, Celestijnenlaan 200G, 3001 Leuven, Belgium. [e-mail].
Drug Design Laboratory, Yokohama City University 1-7-29, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
Biomolecular Architecture, KU Leuven Department of Chemistry, Celestijnenlaan 200F, 3001 Leuven, Belgium.
Laboratory for Bioinorganic Chemistry, KU Leuven Department of Chemistry, Celestijnenlaan 200F, 3001 Leuven, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.47 kDa 
• Atom Count: 2,330 
• Modeled Residue Count: 251 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pizza6S	A	256	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIW (Subject of Investigation/LOI)	B [auth A], C [auth A]	Keggin (STA) O40 Si W12 LFGROBKNYNLKMF-UHFFFAOYSA-B

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.186 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.367	α = 90
b = 44.668	β = 113.28
c = 65.254	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Noguchi, H., Vandebroek, L., Kamata, K., Tame, J.R.H., Van Meervelt, L., Parac-Vogt, T.N., Voet, A.R.D.

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Funding Organization	Location	Grant Number
	Belgium	G0E4717N
	Belgium	G0F9316N
	Belgium	G051917N
	Japan	16H04779

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description