9OSL | pdb_00009osl

Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by ceftriaxone

• PDB DOI: https://doi.org/10.2210/pdb9OSL/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2025-05-24 Released: 2026-06-03 
• Deposition Author(s): Stratton, C.M., Bala, S., Davies, C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Tyrosine-422 plays a crucial role in acylation and transpeptidation in penicillin-binding protein 2 from Neisseria gonorrhoeae

Stratton, C.M., Bala, S., Bivins, M.M., Nicholas, R.A., Davies, C.

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: 35.91 kDa 
• Atom Count: 2,500 
• Modeled Residue Count: 324 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peptidoglycan D,D-transpeptidase PenA	A	330	Neisseria gonorrhoeae	Mutation(s): 1  Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for F2Z7K9 (Neisseria gonorrhoeae) Explore F2Z7K9  Go to UniProtKB:  F2Z7K9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEF (Subject of Investigation/LOI)	B [auth A]	CEFOTAXIME, C3' cleaved, open, bound form C14 H15 N5 O5 S2 NRYMPLKBKFIWQC-YVCCLBOHSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.771	α = 90
b = 59.45	β = 90
c = 112.933	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Stratton, C.M., Bala, S., Davies, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI164794

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release