4QIF | pdb_00004qif

Crystal Structure of PduA with edge mutation K26A and pore mutation S40H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4QIF

This is version 1.4 of the entry. See complete history

Literature

Selective molecular transport through the protein shell of a bacterial microcompartment organelle.

Chowdhury, C.Chun, S.Pang, A.Sawaya, M.R.Sinha, S.Yeates, T.O.Bobik, T.A.

(2015) Proc Natl Acad Sci U S A 112: 2990-2995

  • DOI: https://doi.org/10.1073/pnas.1423672112
  • Primary Citation Related Structures: 
    4QIF, 4QIG, 4RBT, 4RBU, 4RBV

  • PubMed Abstract: 

    Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.


  • Organizational Affiliation
    • Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011;

Macromolecule Content 

  • Total Structure Weight: 97.96 kDa 
  • Atom Count: 6,079 
  • Modeled Residue Count: 791 
  • Deposited Residue Count: 918 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Propanediol utilization protein PduA
A, B, C, D, E
A, B, C, D, E, F, G, H, I
102Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 2 
Gene Names: pduASTM2038
UniProt
Find proteins for P0A1C7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1C7 
Go to UniProtKB:  P0A1C7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1C7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAR

Query on TAR



Download:Ideal Coordinates CCD File
EA [auth G],
U [auth D],
V [auth D]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth F]
GA [auth G]
IA [auth H]
JA [auth H]
AA [auth E],
BA [auth F],
GA [auth G],
IA [auth H],
JA [auth H],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth C],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth F]
FA [auth G]
HA [auth H]
P [auth B]
CA [auth F],
DA [auth F],
FA [auth G],
HA [auth H],
P [auth B],
W [auth D],
Y [auth E],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO

Query on PGO



Download:Ideal Coordinates CCD File
J [auth A],
KA [auth I],
T [auth C]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
K

Query on K



Download:Ideal Coordinates CCD File
O [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.75α = 90
b = 108.75β = 90
c = 334.29γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-03-11
    Changes: Database references
  • Version 1.3: 2015-03-25
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations