6Y7N | pdb_00006y7n

The crystal structure of the eight-bladed symmetrical designer protein Tako8 in the presence of tellurotungstic Anderson-Evans (TEW)

• PDB DOI: https://doi.org/10.2210/pdb6Y7N/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: 1.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.05 kDa 
• Atom Count: 5,470 
• Modeled Residue Count: 638 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.586	α = 90
b = 60.929	β = 90
c = 73.613	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	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: Data collection, Database references, Refinement description