5XGA

Crystal structure of the EnvZ periplasmic domain with CHAPS

• PDB DOI: https://doi.org/10.2210/pdb5XGA/pdb
• Entry: 5XGA supersedes: 5DCJ

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-13 Released: 2017-07-19 
• Deposition Author(s): Hwang, E., Cheong, H.K., Jeon, Y.H., Cheong, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

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

• PubMed: 28423182 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.65 kDa 
• Atom Count: 1,112 
• Modelled Residue Count: 118 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osmolarity sensor protein EnvZ	A	125	Escherichia coli K-12	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	B [auth A], C [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.654	α = 90
b = 45.214	β = 90
c = 70.721	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Hwang, E., Cheong, H.K., Jeon, Y.H., Cheong, C.
• This entry supersedes: 5DCJ

Revision History  

• 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