9TOH | pdb_00009toh

Room temperature serial crystal structure of CTX-M-15 class A beta-lactamase mixed with avibactam for 600 s

• PDB DOI: https://doi.org/10.2210/pdb9TOH/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-16 Released: 2026-10-28 
• Deposition Author(s): Tooke, C.L., Hinchliffe, P., Spencer, J.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Time-resolved ligand dynamics revealed in a beta-lactamase using room-temperature serial crystallography

Tooke, C.L., Hinchliffe, P., Orville, A.M., Spencer, 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: 28.88 kDa 
• Atom Count: 2,286 
• Modeled Residue Count: 259 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaCTX-M-15 EC: 3.5.2.6
UniProt
Find proteins for G3G192 (Klebsiella pneumoniae) Explore G3G192  Go to UniProtKB:  G3G192

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXL (Subject of Investigation/LOI)	D [auth A]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C7 H13 N3 O6 S WJDGWXPPFHLLNL-RITPCOANSA-N
FYG (Subject of Investigation/LOI)	E [auth A]	(2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide C7 H11 N3 O6 S NDCUAPJVLWFHHB-UHNVWZDZSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.273	α = 90
b = 45.986	β = 90
c = 118.829	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Tooke, C.L., Hinchliffe, P., Spencer, J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101021207

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release