Download MendeleyBeta-lactamase from Escherichia coli str. Sakai
Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)To be published.
6N9K
Beta-lactamase from Escherichia coli str. Sakai
- PDB DOI: https://doi.org/10.2210/pdb6N9K/pdb
- Classification: LIGASE
- Organism(s): Escherichia coli O157:H7
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2018-12-03 Released: 2018-12-12
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.156
- R-Value Work: 0.138
- R-Value Observed: 0.138
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 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 | 361 | Escherichia coli O157:H7 | Mutation(s): 0 Gene Names: ampC, ECpv15279_5067, ECs_5131 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for Q8XDQ2 (Escherichia coli O157:H7) Explore Q8XDQ2 Go to UniProtKB: Q8XDQ2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8XDQ2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], G [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A], H [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], F [auth A], I [auth B], J [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSX Query on CSX | A, B | L-PEPTIDE LINKING | C3 H7 N O3 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.156
- R-Value Work: 0.138
- R-Value Observed: 0.138
- Space Group: P 63
- Diffraction Data: https://doi.org/10.18430/m36n9k
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 127.929 | α = 90 |
| b = 127.929 | β = 90 |
| c = 93.02 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data reduction |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-12-12 Deposition Author(s): Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201200026C |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201700060C |
Revision History (Full details and data files)
- Version 1.0: 2018-12-12
Type: Initial release - Version 1.1: 2019-12-18
Changes: Author supporting evidence, Other - Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
