6Y7P | pdb_00006y7p

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.215 (Depositor), 0.217 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 52.05 kDa
Atom Count: 3,084
Modeled Residue Count: 319
Deposited Residue Count: 325
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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	3D Interactions
ZRW (Subject of Investigation/LOI) Query on ZRW Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	W-Zr-cluster H₂ O₆₁ P₂ W₁₇ Zr LRQWFSUELMUBNO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.215 (Depositor), 0.217 (DCC)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.180 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

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: Advisory, Data collection, Database references, Refinement description