9BZR | pdb_00009bzr

Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with clavulonate

• PDB DOI: https://doi.org/10.2210/pdb9BZR/pdb

• Classification: HYDROLASE
• Organism(s): Bordetella bronchiseptica RB50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-24 Released: 2024-06-12 
• Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
• 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: 1.40 Å
• R-Value Free: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

• PubMed: 40391899 
• DOI: https://doi.org/10.1128/mra.00200-25
• Primary Citation Related Structures: 
  5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5UMG, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V0I, 5V36, 5VDN, 5VFB, 5VH6, 5VT3, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NBK, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, ... Search all related entries


• PubMed Abstract: 
  

  Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Biozone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Biosciences Division, University of California, Riverside, School of Medicine, Riverside, California, USA.
Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

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: 29.32 kDa 
• Atom Count: 2,252 
• Modeled Residue Count: 270 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
class A Beta-lactamase, PenP superfamily	A	272	Bordetella bronchiseptica RB50	Mutation(s): 0  Gene Names: BB2049 EC: 3.5.2.6
UniProt
Find proteins for A0A0H3LUA9 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LUA9  Go to UniProtKB:  A0A0H3LUA9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEM (Subject of Investigation/LOI)	C [auth A]	N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE C7 H11 N O3 FXITUJNZFYVSNC-RCYFRSRISA-N
MLA	B [auth A], D [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.255	α = 90
b = 41.914	β = 116.96
c = 78.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

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

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary
• Version 1.2: 2025-09-24
  Changes: Database references