6J4N image
Deposition Date 2019-01-10
Release Date 2019-02-27
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6J4N
Keywords:
Title:
Structure of papua new guinea MBL-1(PNGM-1) native
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Metallo-beta-lactamases PNGM-1
Chain IDs:A, B, C, D, E, F, G, H
Chain Length:372
Number of Molecules:8
Biological Source:uncultured bacterium
Ligand Molecules
Primary Citation
The novel metallo-beta-lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis.
Acta Crystallogr F Struct Biol Commun 74 644 649 (2018)
PMID: 30279316 DOI: 10.1107/S2053230X18012268

Abstact

Metallo-β-lactamases (MBLs) are present in major Gram-negative pathogens and environmental species, and pose great health risks because of their ability to hydrolyze the β-lactam rings of antibiotics such as carbapenems. PNGM-1 was the first reported case of a subclass B3 MBL protein that was identified from a metagenomic library from deep-sea sediments that predate the antibiotic era. In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.10 and 2.30 Å resolution, respectively. Both the native and the selenomethionine-labelled PNGM-1 crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 122, b = 83, c = 163 Å, β = 110°. Matthews coefficient (VM) calculations suggested the presence of 6-10 molecules in the asymmetric unit, corresponding to a solvent content of ∼31-58%. Structure determination is currently in progress.

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Primary Citation of related structures