Download MendeleyFrameshift mutations in genes encoding PBP3 and PBP4 trigger an unusual, extreme beta-lactam resistance phenotype in Burkholderia multivorans
Nukaga, M., Becka, S.A., Zeiser, E.T., Hoshino, Y., LiPuma, J.J., Papp-Wallace, K.M.To be published.
7DDM
Crystal Structure of PenA39 beta-Lactamase
- PDB DOI: https://doi.org/10.2210/pdb7DDM/pdb
- Classification: HYDROLASE
- Organism(s): Burkholderia multivorans CGD2, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-10-29 Released: 2021-11-03
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Veterans Affairs Biomedical Laboratory Research and Development Service, Cystic Fibrosis Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.20 Å
- R-Value Free: 0.144
- R-Value Work: 0.125
- R-Value Observed: 0.126
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-lactamase | 302 | Burkholderia multivorans CGD2 | Mutation(s): 0 Gene Names: BURMUCGD2_4198 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for B9BS30 (Burkholderia multivorans CGD2) Explore B9BS30 Go to UniProtKB: B9BS30 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B9BS30 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ALA-ALA-ARG-ASP-ALA-ALA-VAL-SER-ASP-ALA-ALA-ALA | B [auth E] | 12 | synthetic construct | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| ACT Query on ACT | H [auth A], I [auth A], J [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.20 Å
- R-Value Free: 0.144
- R-Value Work: 0.125
- R-Value Observed: 0.126
- Space Group: P 31
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.519 | α = 90 |
| b = 65.519 | β = 90 |
| c = 51.421 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-11-03 Deposition Author(s): Nukaga, M., Hoshino, T., Papp-Wallace, K.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 20K07484 |
| Veterans Affairs Biomedical Laboratory Research and Development Service | United States | BX002872 |
| Cystic Fibrosis Foundation | United States | LIPUMA13I0 and LIPUMA15P0 |
Revision History (Full details and data files)
- Version 1.0: 2021-11-03
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
