9P0P | pdb_00009p0p

Crystal structure of 23S rRNA methyltransferase Cfr, apoenzyme

• PDB DOI: https://doi.org/10.2210/pdb9P0P/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-06-07 Released: 2025-07-16 
• Deposition Author(s): Stogios, P.J., Skarina, T., Kim, Y., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 23S rRNA methyltransferase Cfr, apoenzyme

Stogios, P.J.

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)

Macromolecule Content 

• Total Structure Weight: 39.91 kDa 
• Atom Count: 2,483 
• Modeled Residue Count: 305 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA large subunit methyltransferase Cfr	A	349	Staphylococcus aureus	Mutation(s): 18  Gene Names: cfr EC: 2.1.1.224
UniProt
Find proteins for A5HBL2 (Staphylococcus aureus) Explore A5HBL2  Go to UniProtKB:  A5HBL2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.319	α = 90
b = 58.612	β = 90
c = 115.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Stogios, P.J., Skarina, T., Kim, Y., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release