6REK | pdb_00006rek

Crystal structure of Pizza6-SH with Cu2+

• PDB DOI: https://doi.org/10.2210/pdb6REK/pdb

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


• Deposited: 2019-04-12 Released: 2019-07-31 
• Deposition Author(s): Noguchi, H., Clarke, D.E., Gryspeerdt, J.L., Feyter, S.D., Voet, A.R.D.
• Funding Organization(s): Research Foundation - Flanders

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.163 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.141 (Depositor) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Artificial beta-propeller protein-based hydrolases.

Clarke, D.E., Noguchi, H., Gryspeerdt, J.A.G., De Feyter, S., Voet, A.R.D.

(2019) Chem Commun (Camb) 55: 8880-8883

• PubMed: 31321399 
• DOI: https://doi.org/10.1039/c9cc04388h
• Primary Citation Related Structures: 
  6REG, 6REH, 6REJ, 6REK, 6REN


• PubMed Abstract: 
  

  We developed an artificial hydrolase based on the symmetrical Pizza6 β-propeller protein for the metal-free hydrolysis of 4-nitrophenyl acetate and butyrate. Through site-specific mutagenesis and crystallisation studies, the catalytic mechanism was investigated and found to be dependent on a threonine-histidine dyad. The mutant with additional histidine residues generated the highest kcat values, forming a His-His-Thr triad and matched previously reported metalloenzymes. The highly symmetrical β-propeller artificial enzymes and their protein-metal complexes have potential to be utilised in bioinorganic and supramolecular chemistry, as well as being developed further into 2D/3D catalytic materials.

---

Organizational Affiliation: 
• Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.16 kDa 
• Atom Count: 2,284 
• Modeled Residue Count: 251 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.163 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.141 (Depositor) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.708	α = 90
b = 69.547	β = 109.16
c = 48.266	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Noguchi, H., Clarke, D.E., Gryspeerdt, J.L., Feyter, S.D., Voet, A.R.D.

---

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	G0E4717N, G0F9316N, G051917N

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description