2FGT | pdb_00002fgt

Crystal Structure of YycH from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2FGT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-22 Released: 2006-04-25 
• Deposition Author(s): Szurmant, H., Zhao, H., Mohan, M.A., James, H.A., Varughese, K.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.304 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Literature

The crystal structure of YycH involved in the regulation of the essential YycFG two-component system in Bacillus subtilis reveals a novel tertiary structure.

Szurmant, H., Zhao, H., Mohan, M.A., Hoch, J.A., Varughese, K.I.

(2006) Protein Sci 15: 929-934

• PubMed: 16600972 
• DOI: https://doi.org/10.1110/ps.052064406
• Primary Citation Related Structures: 
  2FGT


• PubMed Abstract: 
  

  The Bacillus subtilis YycFG two-component signal transduction system is essential for cell viability, and the YycH protein is part of the regulatory circuit that controls its activity. The crystal structure of YycH was solved by two-wavelength selenium anomalous dispersion data, and was refined using 2.3 A data to an R-factor of 25.2%. The molecule is made up of three domains, and has a novel three-dimensional structure. The N-terminal domain features a calcium binding site and the central domain contains two conserved loop regions.

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Organizational Affiliation: 
• Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.94 kDa 
• Atom Count: 3,058 
• Modeled Residue Count: 373 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-component system yycF/yycG regulatory protein yycH	A	417	Bacillus subtilis	Mutation(s): 0  Gene Names: yycH
UniProt
Find proteins for Q794W0 (Bacillus subtilis (strain 168)) Explore Q794W0  Go to UniProtKB:  Q794W0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.304 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.578	α = 90
b = 63.578	β = 90
c = 192.327	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Szurmant, H., Zhao, H., Mohan, M.A., James, H.A., Varughese, K.I.

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references