8EO6

Crystal structure of metagenomic class A beta-lactamase precursor LRA-5 in complex with ceftazidime at 2.35 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8EO6/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): uncultured soil bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-02 Released: 2023-10-04 
• Deposition Author(s): Power, P., D'Amico Gonzalez, G., Centron, D., Gutkind, G., Handelsman, J., Klinke, S.
• Funding Organization(s): National Scientific and Technical Research Council (CONICET), Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.216 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Playing beta-Lactamase Evolution: Metagenomic Class A beta-Lactamase LRA-5 is an Inactive Enzyme Capable of Rendering an Active beta-Lactamase by Introduction of Y69Q and V166E Substitutions

D'Amico Gonzalez, G., Handelsman, J., Centron, D., Gutkind, G., Klinke, S., Power, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.89 kDa 
• Atom Count: 4,120 
• Modelled Residue Count: 536 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LRA-5	A, B	290	uncultured soil bacterium	Mutation(s): 0  Gene Names: blaLRA-5, AKSOIL_0013
UniProt
Find proteins for B5L5W7 (uncultured bacterium BLR5) Explore B5L5W7  Go to UniProtKB:  B5L5W7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAZ (Subject of Investigation/LOI)	C [auth A], D [auth B]	ACYLATED CEFTAZIDIME C17 H19 N5 O7 S2 VEHPZKIFULQYFS-BZXVCXBKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.216 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.08	α = 90
b = 162.11	β = 90
c = 70.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Power, P., D'Amico Gonzalez, G., Centron, D., Gutkind, G., Handelsman, J., Klinke, S.

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Funding Organization	Location	Grant Number
National Scientific and Technical Research Council (CONICET)	Argentina	11220200100191CO
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2018 01550

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release