2ZWM | pdb_00002zwm

Crystal structure of YycF receiver domain from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2ZWM/pdb

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


• Deposited: 2008-12-16 Released: 2009-07-14 
• Deposition Author(s): Doi, A., Okajima, T., Utsumi, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Novel Antibiotics Target Protein of Gram-positive Pathogens: X-ray Crystal Structures and Search of Potential Drug-Binding sites

Doi, A., Okajima, T., Gotoh, Y., Tanizawa, K., Utsumi, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.53 kDa 
• Atom Count: 2,005 
• Modeled Residue Count: 240 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein yycF	A, B	130	Bacillus subtilis	Mutation(s): 0  Gene Names: yycF
UniProt
Find proteins for P37478 (Bacillus subtilis (strain 168)) Explore P37478  Go to UniProtKB:  P37478

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.824	α = 90
b = 58.824	β = 90
c = 78.247	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Doi, A., Okajima, T., Utsumi, R.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description