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 1.4 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: 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Permuted PduAA, B, C, D, E90synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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

View Full Validation Report




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