3CGI

Crystal structure of the PduU shell protein from the Pdu microcompartment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the PduU Shell Protein from the Pdu Microcompartment of Salmonella

Crowley, C.S.Sawaya, M.R.Bobik, T.A.Yeates, T.O.

(2008) Structure 16: 1324-1332

  • DOI: https://doi.org/10.1016/j.str.2008.05.013
  • Primary Citation of Related Structures:  
    3CGI

  • PubMed Abstract: 

    The Pdu microcompartment is a proteinaceous, subcellular structure that serves as an organelle for the metabolism of 1,2-propanediol in Salmonella enterica. It encapsulates several related enzymes within a shell composed of a few thousand protein subunits. Recent structural studies on the carboxysome, a related microcompartment involved in CO(2) fixation, have concluded that the major shell proteins from that microcompartment form hexamers that pack into layers comprising the facets of the shell. Here we report the crystal structure of PduU, a protein from the Pdu microcompartment, representing the first structure of a shell protein from a noncarboxysome microcompartment. Though PduU is a hexamer like other characterized shell proteins, it has undergone a circular permutation leading to dramatic differences in the hexamer pore. In view of the hypothesis that microcompartment metabolites diffuse across the outer shell through these pores, the unique structure of PduU suggests the possibility of a special functional role.


  • Organizational Affiliation

    University of California Los Angeles Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propanediol utilization protein pduU
A, B, C, D
124Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: pduU
UniProt
Find proteins for P0A1D1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1D1 
Go to UniProtKB:  P0A1D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1D1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.14α = 90
b = 74.14β = 90
c = 218.021γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description