Download MendeleyOXA-58 crystal structure of acylated meropenem complex 2
Saino, H., Sugiyabu, T., Miyano, M.To be published.
7VX3 | pdb_00007vx3
7VX3 | pdb_00007vx3
OXA-58 crystal structure of acylated meropenem complex 2
- PDB DOI: https://doi.org/10.2210/pdb7VX3/pdb
- Classification: HYDROLASE
- Organism(s): Acinetobacter baumannii
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2021-11-12 Released: 2022-11-23
- Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.163 (Depositor), 0.164 (DCC)
- R-Value Work: 0.146 (Depositor), 0.143 (DCC)
- R-Value Observed: 0.169 (Depositor)
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-lactamase | 280 | Acinetobacter baumannii | Mutation(s): 0 Gene Names: blaOXA-58, bla-oxa-58, bla-oxa58 EC: 3.5.2.6 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2TR58 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DWZ (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | D [auth A] | (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-VGWSNGFZSA-N |  | ||
| MER (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | C [auth A] | (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d
ihydro-1H-pyrrole-2-carboxylic acid C17 H27 N3 O5 S DYQHXZPAIVAJRU-HTXLXMOSSA-N |  | ||
| SO4 Download:Ideal Coordinates CCD File | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KCX Query on KCX | A | L-PEPTIDE LINKING | C7 H14 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.163 (Depositor), 0.164 (DCC)
- R-Value Work: 0.146 (Depositor), 0.143 (DCC)
- R-Value Observed: 0.169 (Depositor)
Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 75.29 | α = 90 |
| b = 75.29 | β = 90 |
| c = 119.47 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| iMOSFLM | data reduction |
| MOLREP | phasing |
| CrystalClear | data collection |
| iMOSFLM | data scaling |
Entry History
& Funding InformationDeposition Data
- Released Date: 2022-11-23 Deposition Author(s): Saino, H., Sugiyabu, T., Miyano, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology (Japan) | Japan | S1311005 |
| Ministry of Education, Culture, Sports, Science and Technology (Japan) | Japan | 18K07118 |
Revision History (Full details and data files)
- Version 1.0: 2022-11-23
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
