6W2Z

Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam

• PDB DOI: https://doi.org/10.2210/pdb6W2Z/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-08 Released: 2020-03-25 
• Deposition Author(s): Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• 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: 1.50 Å
• R-Value Free: 0.199 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam

Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.84 kDa 
• Atom Count: 4,451 
• Modelled Residue Count: 521 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	275	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: penP, BSU18800 EC: 3.5.2.6
UniProt
Find proteins for P39824 (Bacillus subtilis (strain 168)) Explore P39824  Go to UniProtKB:  P39824

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXL (Subject of Investigation/LOI)	C [auth A], F [auth B]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C7 H13 N3 O6 S WJDGWXPPFHLLNL-RITPCOANSA-N
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.199 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.681	α = 90
b = 85.456	β = 94.969
c = 70.36	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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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: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary