4WBG | pdb_00004wbg

Crystal structure of class C beta-lactamase Mox-1 covalently complexed with aztorenam

• PDB DOI: https://doi.org/10.2210/pdb4WBG/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-03 Released: 2015-07-01 
• Deposition Author(s): Oguri, T., Shimizu-ibuka, A., Ishii, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Conformational Change Observed in the Active Site of Class C beta-Lactamase MOX-1 upon Binding to Aztreonam

Oguri, T., Ishii, Y., Shimizu-Ibuka, A.

(2015) Antimicrob Agents Chemother 59: 5069-5072

• PubMed: 26055361 
• DOI: https://doi.org/10.1128/AAC.04428-14
• Primary Citation Related Structures: 
  4WBG


• PubMed Abstract: 
  

  We solved the crystal structure of the class C β-lactamase MOX-1 complexed with the inhibitor aztreonam at 1.9Å resolution. The main-chain oxygen of Ser315 interacts with the amide nitrogen of aztreonam. Surprisingly, compared to that in the structure of free MOX-1, this main-chain carboxyl changes its position significantly upon binding to aztreonam. This result indicates that the interaction between MOX-1 and β-lactams can be accompanied by conformational changes in the B3 β-strand main chain.

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Organizational Affiliation: 
• Department of Science, Yamagata University, Yamagata, Japan.
Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan.
Department of Science, Yamagata University, Yamagata, Japan Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan [e-mail].

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: 41.66 kDa 
• Atom Count: 2,836 
• Modeled Residue Count: 347 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	380	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaMOX-1 EC: 3.5.2.6
UniProt
Find proteins for Q51578 (Klebsiella pneumoniae) Explore Q51578  Go to UniProtKB:  Q51578

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZR	B [auth A]	2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid C13 H19 N5 O8 S2 OEVQTUTXOVDNJO-GEEOIBTQSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	J [auth A], K [auth A], L [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.54	α = 90
b = 59.25	β = 102.72
c = 62.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Oguri, T., Shimizu-ibuka, A., Ishii, Y.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 1.2: 2020-01-29
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary