6BQX

Crystal structure of Escherichia coli DsbA in complex with N-methyl-1-(4-phenoxyphenyl)methanamine

• PDB DOI: https://doi.org/10.2210/pdb6BQX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-11-29 Released: 2017-12-27 
• Deposition Author(s): Heras, B., Totsika, M., Paxman, J.J., Wang, G., Scanlon, M.J.
• Funding Organization(s): Australian Research Council (ARC), Australian Synchrotron Research Program Fellowship

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.244 
• R-Value Work: 0.176 
• R-Value Observed: 0.183 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4wf5

Literature

Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens.

Totsika, M., Vagenas, D., Paxman, J.J., Wang, G., Dhouib, R., Sharma, P., Martin, J.L., Scanlon, M.J., Heras, B.

(2018) Antioxid Redox Signal 29: 653-666

• PubMed: 29237285 
• DOI: https://doi.org/10.1089/ars.2017.7104
• Primary Citation of Related Structures:  
  6BQX, 6BR4


• PubMed Abstract: 
  

  DsbA catalyzes disulfide bond formation in secreted and outer membrane proteins in bacteria. In pathogens, DsbA is a major facilitator of virulence constituting a target for antivirulence antimicrobial development. However, many pathogens encode multiple and diverse DsbA enzymes for virulence factor folding during infection. The aim of this study was to determine whether our recently identified inhibitors of Escherichia coli K-12 DsbA can inhibit the diverse DsbA enzymes found in two important human pathogens and attenuate their virulence.

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Organizational Affiliation: 

1 Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology , Queensland, Australia .

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.52 kDa 
• Atom Count: 3,197 
• Modelled Residue Count: 375 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B	189	Escherichia coli K-12	Mutation(s): 0  Gene Names: dsbA, dsf, ppfA, b3860, JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9AG	C [auth A]	N-methyl-1-(4-phenoxyphenyl)methanamine C14 H15 N O YWBKPTGYRUSBFV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.244 
• R-Value Work: 0.176 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.15	α = 90
b = 64.901	β = 126.53
c = 75.416	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Heras, B., Totsika, M., Paxman, J.J., Wang, G., Scanlon, M.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP150102287
Australian Research Council (ARC)	Australia	FT130100580
Australian Synchrotron Research Program Fellowship	Australia	--

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2018-08-08
  Changes: Data collection, Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence