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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tako8	A, B	325	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Parac-Vogt, T.N.

Van Meervelt, L.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.