3PAC

Crystal structure of PduT a trimeric bacterial microcompartment protein with 4Fe-4S cluster binding site

PDB DOI: https://doi.org/10.2210/pdb3PAC/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Citrobacter freundii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-19 Released: 2010-12-01
Deposition Author(s): Pang, A.H., Warren, M.J., Pickersgill, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.252
R-Value Work: 0.199
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site

Pang, A., Warren, M.J., Pickersgill, R.W.

(2011) Acta Crystallogr D Biol Crystallogr 67: 91-96

PubMed: 21245529 Search on PubMed
DOI: https://doi.org/10.1107/S0907444910050201
Primary Citation of Related Structures:
3PAC

PubMed Abstract:
Propanediol metabolism in Citrobacter freundii occurs within a metabolosome, a subcellular proteinaceous bacterial microcompartment. The propanediol-utilization (Pdu) microcompartment shell is constructed from thousands of hexagonal-shaped protein complexes made from seven different types of protein subunit. Here, the structure of the bacterial microcompartment protein PduT, which has a tandem structural repeat within the subunit and forms trimers with pseudo-hexagonal symmetry, is reported. This trimeric assembly forms a flat approximately hexagonally shaped disc with a central pore that is suitable for a 4Fe-4S cluster. The essentially cubic shaped 4Fe-4S cluster conforms to the threefold symmetry of the trimer with one free iron, the role of which could be to supply electrons to an associated microcompartment enzyme, PduS.

Organizational Affiliation

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England.

Macromolecule Content

Total Structure Weight: 21.23 kDa
Atom Count: 1,363
Modelled Residue Count: 183
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shell protein	A	204	Citrobacter freundii	Mutation(s): 0 Gene Names: pduT
UniProt
Find proteins for B1VB78 (Citrobacter freundii) Explore B1VB78 Go to UniProtKB: B1VB78
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1VB78
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.252
R-Value Work: 0.199
R-Value Observed: 0.204
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.68	α = 90
b = 67.68	β = 90
c = 62.03	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Pickersgill, R.W.

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.