4UZM | pdb_00004uzm

Shotgun proteolysis: A practical application

• PDB DOI: https://doi.org/10.2210/pdb4UZM/pdb
• BMRB: 25210

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-05 Released: 2014-09-17 
• Deposition Author(s): Allen, M.D., Bycroft, M., Freund, S.M.V., Christ, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: NO VIOLATIONS 

Literature

Solution Structure of a Soluble Fragment Derived from a Membrane Protein by Shotgun Proteolysis.

Allen, M.D., Christie, M., Jones, P., Porebski, B.T., Roome, B., Freund, S.M., Buckle, A.M., Bycroft, M., Christ, D.

(2015) Protein Eng Des Sel 28: 445

• PubMed: 25877662 
• DOI: https://doi.org/10.1093/protein/gzv021
• Primary Citation Related Structures: 
  4UZM


• PubMed Abstract: 
  

  We have previously reported a phage display method for the identification of protein domains on a genome-wide scale (shotgun proteolysis). Here we present the solution structure of a fragment of the Escherichia coli membrane protein yrfF, as identified by shotgun proteolysis, and determined by NMR spectroscopy. Despite the absence of computational predictions, the fragment formed a well-defined beta-barrel structure, distantly falling within the OB-fold classification. Our results highlight the potential of high-throughput experimental approaches for the identification of protein domains for structural studies.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia Faculty of Medicine, St Vincent's Clinical School, The University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia.
Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia Faculty of Medicine, St Vincent's Clinical School, The University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.44 kDa 
• Atom Count: 938 
• Modeled Residue Count: 119 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE MEMBRANE PROTEIN IGAA HOMOLOG	A	120	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P45800 (Escherichia coli (strain K12)) Explore P45800  Go to UniProtKB:  P45800

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: NO VIOLATIONS 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Allen, M.D., Bycroft, M., Freund, S.M.V., Christ, D.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Atomic model
• Version 1.2: 2015-04-29
  Changes: Database references, Other
• Version 1.3: 2015-10-21
  Changes: Database references
• Version 1.4: 2016-04-27
  Changes: Atomic model, Other
• Version 1.5: 2024-05-15
  Changes: Data collection, Database references, Other