2ZXJ | pdb_00002zxj

Crystal structure of YycF DNA-binding domain from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb2ZXJ/pdb
• Entry: 2ZXJ supersedes: 2Z9M

• Classification: TRANSCRIPTION
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-26 Released: 2009-01-20 
• Deposition Author(s): Okajima, T., Doi, A., Utsumi, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.240 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.189 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.83 kDa 
• Atom Count: 1,844 
• Modeled Residue Count: 200 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein walR	A, B	120	Staphylococcus aureus	Mutation(s): 0  Gene Names: yycF
UniProt
Find proteins for Q9RDT5 (Staphylococcus aureus) Explore Q9RDT5  Go to UniProtKB:  Q9RDT5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.240 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.634	α = 90
b = 45.556	β = 103.52
c = 78.043	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Okajima, T., Doi, A., Utsumi, R.
• This entry supersedes: 2Z9M

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description