7OV7 | pdb_00007ov7

The hybrid cage formed between Pizza6-S and Cu(II)-substituted trilacunary Keggin

PDB DOI: https://doi.org/10.2210/pdb7OV7/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-14 Released: 2022-04-27
Deposition Author(s): Vandebroek, L., Noguchi, H., Anyushin, A., Van Meervelt, L., Voet, A.R.D., Parac-Vogt, T.N.
Funding Organization(s): KU Leuven, Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.287 (Depositor), 0.296 (DCC)
R-Value Work:
0.232 (Depositor), 0.244 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Hierarchical Self-Assembly of a Supramolecular Protein-Metal Cage Encapsulating a Polyoxometalate Guest

Vandebroek, L., Noguchi, H., Anyushin, A., Van Meervelt, L., Voet, A.R.D., Parac-Vogt, T.N.

(2022) Cryst Growth Des

DOI: https://doi.org/10.1021/acs.cgd.1c01138

Macromolecule Content

Total Structure Weight: 56.51 kDa
Atom Count: 3,987
Modeled Residue Count: 499
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pizza6-S	A, B	256	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PW9 (Subject of Investigation/LOI) Query on PW9 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A]	I [auth A], P [auth B]	Trilacunary Keggin O₃₄ P W₉ FITSDOGSJOFYAU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.287 (Depositor), 0.296 (DCC)
R-Value Work: 0.232 (Depositor), 0.244 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.792	α = 90
b = 74.15	β = 90
c = 79.733	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

Deposition Author(s):

Funding Organization	Location	Grant Number
KU Leuven	Belgium	PDM/20/093
Research Foundation - Flanders (FWO)	Belgium	G0E4717N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N