5HPN | pdb_00005hpn

A circularly permuted PduA forming an icosahedral cage

• PDB DOI: https://doi.org/10.2210/pdb5HPN/pdb

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


• Deposited: 2016-01-20 Released: 2016-04-06 
• Deposition Author(s): Leibly, D.J., Jorda, J., Yeates, T.O.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.256 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein.

Jorda, J., Leibly, D.J., Thompson, M.C., Yeates, T.O.

(2016) Chem Commun (Camb) 52: 5041-5044

• PubMed: 26988700 
• DOI: https://doi.org/10.1039/c6cc00851h
• Primary Citation Related Structures: 
  5HPN


• PubMed Abstract: 
  

  We report the crystal structure of a novel 60-subunit dodecahedral cage that results from self-assembly of a re-engineered version of a natural protein (PduA) from the Pdu microcompartment shell. Biophysical data illustrate the dependence of assembly on solution conditions, opening up new applications in microcompartment studies and nanotechnology.

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Organizational Affiliation: 
• UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.99 kDa 
• Atom Count: 2,890 
• Modeled Residue Count: 424 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Permuted PduA	A, B, C, D, E	90	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.256 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.5	α = 90
b = 144.5	β = 90
c = 144.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Leibly, D.J., Jorda, J., Yeates, T.O.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1332907

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-04-13
  Changes: Database references
• Version 1.2: 2016-04-20
  Changes: Derived calculations
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description