7CX5

Crystal structure of the DNA-binding domain of Bacillus subtilis CssR

• PDB DOI: https://doi.org/10.2210/pdb7CX5/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-01 Released: 2021-04-21 
• Deposition Author(s): Dahal, P., Kim, D.Y., Kwon, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.204 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Crystal structure of the DNA-binding domain of Bacillus subtilis CssR.

Dahal, P., Kim, D.Y., Kwon, E.

(2021) Biochem Biophys Res Commun 555: 26-31

• PubMed: 33812055 
• DOI: https://doi.org/10.1016/j.bbrc.2021.03.101
• Primary Citation of Related Structures:  
  7CX5


• PubMed Abstract: 
  

  Bacteria utilize two-component systems to regulate gene expression in response to changes in environmental stimuli. CssS/CssR, a two-component system in Bacillus subtilis, is responsible for overcoming envelope stresses caused by heat shock and secretion overload. During stress, the sensor component CssS is auto-phosphorylated and transfers the phosphoryl group to the response regulator CssR. Phosphorylated CssR then directly regulates the transcription of genes required to counteract the stress. Here, the crystal structure of the DNA-binding domain of CssR, determined at 1.07 Å resolution, is reported. The structure shows that the DNA-binding domain of CssR harbors a winged helix-turn-helix motif that is conserved in the OmpR/PhoB subfamily of response regulators. Based on the crystal structure, the dimeric architecture of the full-length CssR and its DNA-binding mode were suggested.

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Organizational Affiliation: 

College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 11.16 kDa 
• Atom Count: 882 
• Modelled Residue Count: 88 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein CssR	A	95	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: cssR, BSU33010
UniProt
Find proteins for O32192 (Bacillus subtilis (strain 168)) Explore O32192  Go to UniProtKB:  O32192

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.204 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.41	α = 90
b = 52.74	β = 90
c = 58.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Dahal, P., Kim, D.Y., Kwon, E.

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references