3F6P | pdb_00003f6p

Crystal Structure of unphosphorelated receiver domain of YycF

• PDB DOI: https://doi.org/10.2210/pdb3F6P/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-06 Released: 2010-03-02 
• Deposition Author(s): Zhao, H., Tang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.243 (DCC) 

Starting Model: experimental

Literature

Preliminary crystallographic studies of the regulatory domain of response regulator YycF from an essential two-component signal transduction system.

Zhao, H., Heroux, A., Sequeira, R.D., Tang, L.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 719-722

• PubMed: 19574649 
• DOI: https://doi.org/10.1107/S1744309109022696
• Primary Citation Related Structures: 
  3F6P


• PubMed Abstract: 
  

  YycGF is a crucial signal transduction system for the regulation of cell-wall metabolism in low-G+C Gram-positive bacteria, which include many important human pathogens. The response regulator YycF receives signals from its cognate histidine kinase YycG through a phosphotransfer reaction and elicits responses through regulation of gene expression. The N-terminal regulatory domain of YycF from Bacillus subtilis was overproduced and purified. The protein was crystallized and X-ray data were collected to 1.95 A resolution with a completeness of 97.7% and an overall R(merge) of 7.7%. The crystals belonged to space group P3(1)21, with unit-cell parameters a = b = 59.50, c = 79.06 A.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.79 kDa 
• Atom Count: 988 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein yycF	A	120	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU40410, yycF
UniProt
Find proteins for P37478 (Bacillus subtilis (strain 168)) Explore P37478  Go to UniProtKB:  P37478

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.243 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.495	α = 90
b = 59.495	β = 90
c = 79.059	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Zhao, H., Tang, L.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description