5CHB

Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal

• PDB DOI: https://doi.org/10.2210/pdb5CHB/pdb
• Entry: 5CHB supersedes: 4ZCO

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2015-07-22 
• Deposition Author(s): Voet, A.R.D., Noguchi, H., Addy, C., Zhang, K.Y.J., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein

Voet, A.R.D., Noguchi, H., Addy, C., Zhang, K.Y.J., Tame, J.R.H.

(2015) Angew Chem Int Ed Engl 54: 9857-9860

• PubMed: 26136355 
• DOI: https://doi.org/10.1002/anie.201503575
• Primary Citation of Related Structures:  
  5CHB


• PubMed Abstract: 
  

  We have engineered a metal-binding site into the novel artificial β-propeller protein Pizza. This new Pizza variant carries two nearly identical domains per polypeptide chain, and forms a trimer with three-fold symmetry. The designed single metal ion binding site lies on the symmetry axis, bonding the trimer together. Two copies of the trimer associate in the presence of cadmium chloride in solution, and very high-resolution X-ray crystallographic analysis reveals a nanocrystal of cadmium chloride, sandwiched between two trimers of the protein. This nanocrystal, containing seven cadmium ions lying in a plane and twelve interspersed chloride ions, is the smallest reported to date. Our results indicate the feasibility of using rationally designed symmetrical proteins to biomineralize nanocrystals with useful properties.

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Organizational Affiliation: 

Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045 (Japan). [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 27.43 kDa 
• Atom Count: 2,014 
• Modelled Residue Count: 254 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nvPizza2-S16H58	A, B, C	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	D [auth A], E [auth B], F [auth B], G [auth B], L [auth C], M [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth B], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.2	α = 90
b = 61.2	β = 90
c = 109.558	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Voet, A.R.D., Noguchi, H., Addy, C., Zhang, K.Y.J., Tame, J.R.H.
• This entry supersedes: 4ZCO

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 1.2: 2017-10-04
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description