9JSE | pdb_00009jse

Crystal Structure of PenI beta-Lactamase from Burkholderia pseudomallei Complex with Taniborbactam

• PDB DOI: https://doi.org/10.2210/pdb9JSE/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei K96243
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-30 Released: 2025-08-13 
• Deposition Author(s): Nukaga, M., Hoshino, T., Mojica, M.F., Papp-Wallace, K.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Wellcome Trust, Department of Health & Human Services (HHS), Department of Veterans Affairs (VA, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.151 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Burkholderia pseudomallei PenI beta-lactamase and Variants Are Potently Inhibited by Taniborbactam

Mojica, M.F., Hoshino, T., Papp-Wallace, K.M., Nukaga, M.

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: 28.6 kDa 
• Atom Count: 2,348 
• Modeled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	264	Burkholderia pseudomallei K96243	Mutation(s): 0  Gene Names: penA, blaA, BPSS0946 EC: 3.5.2.6
UniProt
Find proteins for H7C785 (Burkholderia pseudomallei (strain K96243)) Explore H7C785  Go to UniProtKB:  H7C785

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KJK (Subject of Investigation/LOI)	B [auth A]	(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid C19 H28 B N3 O5 PFZUWUXKQPRWAL-NOLJZWGESA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.151 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.202	α = 90
b = 52.12	β = 92.554
c = 50.436	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Nukaga, M., Hoshino, T., Mojica, M.F., Papp-Wallace, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201300019C
Wellcome Trust	United Kingdom	360G-Wellcome-101999/Z/13/Z
Department of Health & Human Services (HHS)	United States	HHSO100201900007C
Department of Veterans Affairs (VA, United States)	United States	BX002872

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release