8EP6

Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in complex with Avibactam

• PDB DOI: https://doi.org/10.2210/pdb8EP6/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Chitinophaga pinensis DSM 2588
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-05 Released: 2022-10-19 
• Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), 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: 1.50 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in the complex with Avibactam.

Maltseva, N., Kim, Y., Endres, M., Joachimiak, A.

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: 29.94 kDa 
• Atom Count: 2,211 
• Modelled Residue Count: 245 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Class D Cpin_0907	A	247	Chitinophaga pinensis DSM 2588	Mutation(s): 0  Gene Names: blaOXA, FEF09_01595
UniProt
Find proteins for A0A5C6M0R4 (Chitinophaga pinensis) Explore A0A5C6M0R4  Go to UniProtKB:  A0A5C6M0R4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXL (Subject of Investigation/LOI)	B [auth A]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C7 H13 N3 O6 S WJDGWXPPFHLLNL-RITPCOANSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.816	α = 90
b = 67.864	β = 90
c = 68.698	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), 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: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Other, Structure summary