6Y7P

The complex between the eight-bladed symmetrical designer protein Tako8 and 1:2 zirconium(IV) Wells-Dawson (ZrWD)

• PDB DOI: https://doi.org/10.2210/pdb6Y7P/pdb

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


• Deposited: 2020-03-02 Released: 2020-12-16 
• Deposition Author(s): Vandebroek, L., Noguchi, H., Parac-Vogt, T.N., Van Meervelt, L., Voet, A.R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Shape and Size Complementarity-Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters

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

(2021) Cryst Growth Des 

• DOI: https://doi.org/10.1021/acs.cgd.0c01571

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 52.05 kDa 
• Atom Count: 3,084 
• Modelled Residue Count: 319 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tako8	A	325	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZRW (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	W-Zr-cluster H2 O61 P2 W17 Zr LRQWFSUELMUBNO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.347	α = 90
b = 72.799	β = 120.38
c = 54.288	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Vandebroek, L., Noguchi, H., Parac-Vogt, T.N., Van Meervelt, L., Voet, A.R.D.

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description