8EO7

Crystal structure of metagenomic beta-lactamase LRA-5 Y69Q/V166E mutant at 2.15 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8EO7/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): uncultured soil bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.225
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 61.94 kDa
Atom Count: 3,858
Modelled Residue Count: 503
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	290	uncultured soil bacterium	Mutation(s): 2
UniProt
Find proteins for B5L5W7 (uncultured bacterium BLR5) Go to UniProtKB: B5L5W7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.225
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.861	α = 90
b = 162.236	β = 90
c = 70.277	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

D'Amico Gonzalez, G.

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.