5HPN

A circularly permuted PduA forming an icosahedral cage

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1039/c6cc00851h
  • Primary Citation of 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.

    • Organizational Affiliation: 

    UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA. yeates@mbi.ucla.edu.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Permuted PduA
A, B, C, D, E
90synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.5α = 90
b = 144.5β = 90
c = 144.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1332907

Revision History  (Full details and data files)

  • 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