5XGA | pdb_00005xga

Crystal structure of the EnvZ periplasmic domain with CHAPS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Crystal structure of the EnvZ periplasmic domain with CHAPS.

Hwang, E., Cheong, H.K., Kim, S.Y., Kwon, O., Blain, K.Y., Choe, S., Yeo, K.J., Jung, Y.W., Jeon, Y.H., Cheong, C.

(2017) FEBS Lett 591: 1419-1428

  • DOI: https://doi.org/10.1002/1873-3468.12658
  • Primary Citation of Related Structures:  
    5XGA

  • PubMed Abstract: 

    Bacteria sense and respond to osmolarity through the EnvZ-OmpR two-component system. The structure of the periplasmic sensor domain of EnvZ (EnvZ-PD) is not available yet. Here, we present the crystal structure of EnvZ-PD in the presence of CHAPS detergent. The structure of EnvZ-PD shows similar folding topology to the PDC domains of PhoQ, DcuS, and CitA, but distinct orientations of helices and β-hairpin structures. The CD and NMR spectra of EnvZ-PD in the presence of cholate, a major component of bile salts, are similar to those with CHAPS. Chemical cross-linking shows that the dimerization of EnvZ-PD is significantly inhibited by the CHAPS and cholate. Together with β-galactosidase assay, these results suggest that bile salts may affect the EnvZ structure and function in Escherichia coli.

    • Organizational Affiliation: 

    Division of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Chungbuk, Korea.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Osmolarity sensor protein EnvZ125Escherichia coli K-12Mutation(s): 0 
Gene Names: envZ, ompB, perA, tpo, b3404, JW3367
EC: 2.7.13.3
UniProt
Find proteins for P0AEJ4 (Escherichia coli (strain K12))
Explore P0AEJ4 
Go to UniProtKB:  P0AEJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEJ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.654α = 90
b = 45.214β = 90
c = 70.721γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPSClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references