5F53

Nano-ring of cadmium ions coordinated by nvPizza2-S16S58

• PDB DOI: https://doi.org/10.2210/pdb5F53/pdb

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


• Deposited: 2015-12-04 Released: 2016-12-14 
• Deposition Author(s): Voet, A.R.D., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

A cadmium chloride ring created by a designed symmetrical protein

Voet, A.R.D., Terada, D., Noguchi, H., Addy, C., Unzai, S., Akashi, S., Zhang, K.Y.J., Tame, J.R.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 8.95 kDa 
• Atom Count: 649 
• Modelled Residue Count: 84 
• Deposited Residue Count: 87 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NVPIZZA2-S16S58	A	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.32	α = 90
b = 110.32	β = 90
c = 110.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Voet, A.R.D., Tame, J.R.H.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations