8EO6 | pdb_00008eo6

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 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: 62.89 kDa
Atom Count: 4,120
Modeled Residue Count: 536
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5L5W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAZ (Subject of Investigation/LOI) Query on CAZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ACYLATED CEFTAZIDIME C₁₇ H₁₉ N₅ O₇ S₂ VEHPZKIFULQYFS-BZXVCXBKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

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

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Ligand Structure Quality Assessment

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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
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.