6E8A

Crystal structure of DcrB from Salmonella enterica at 1.92 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of DcrB, a lipoprotein from Salmonella enterica, reveals flexibility in the N-terminal segment of the Mog1p/PsbP-like fold.

Rasmussen, D.M.Soens, R.W.Davie, T.J.Vaneerd, C.K.Bhattacharyya, B.May, J.F.

(2018) J Struct Biol 204: 513-518

  • DOI: https://doi.org/10.1016/j.jsb.2018.10.005
  • Primary Citation of Related Structures:  
    6E8A

  • PubMed Abstract: 

    DcrB is an 18 kDa lipoprotein that contains a single domain of unknown function. DcrB is found within Enterobacteriaceae, a family of Gram-negative bacteria which includes pathogens that can cause food-borne illness and hospital-acquired infections. In Salmonella enterica serovar Typhimurium, DcrB is up-regulated by conditions that promote the production of known virulence factors. We determined the structure of a truncated form of DcrB from Salmonella to 1.92 Å resolution by X-ray crystallography. This truncated form, DcrBΔ37, contains the entire domain of unknown function but lacks the lipoprotein signal sequence (residues 1-20) as well as residues 21-37. The DcrBΔ37 monomer contains the Mog1p/PsbP-like fold, which is found in functionally diverse proteins in mammals, yeast, plants, and cyanobacteria. Interestingly, DcrBΔ37 crystallized as a domain-swapped homodimer in which the N-terminal β-hairpin extends from one protomer to interact with the core of the second protomer. This domain-swapping indicates that the N-terminal portion of the Mog1p/PsbP-like fold likely has conformational flexibility. Overall, our results provide the first example of an enterobacterial protein that contains the Mog1p/PsbP-like fold and expands knowledge of the structural and phylogenetic diversity of Mog1p/PsbP-like proteins.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1795 domain-containing protein
A, B
156Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: C4822_00510C4872_00325DD95_06545
UniProt
Find proteins for Q7CPJ3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q7CPJ3 
Go to UniProtKB:  Q7CPJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CPJ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.715α = 90
b = 41.715β = 90
c = 533.438γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description