Download MendeleyCrystal Structure of Beta-lactamase class D from Bacillus subtilis
Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
5E2F | pdb_00005e2f
Crystal Structure of Beta-lactamase class D from Bacillus subtilis
- PDB DOI: https://doi.org/10.2210/pdb5E2F/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus subtilis subsp. subtilis str. 168
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2015-10-01 Released: 2015-10-14
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.152 (Depositor), 0.150 (DCC)
- R-Value Work: 0.125 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.126 (Depositor)
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 YbxI | 270 | Bacillus subtilis subsp. subtilis str. 168 | Mutation(s): 0 Gene Names: ybxI, ybdS, BSU02090 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for P54427 (Bacillus subtilis (strain 168)) Explore P54427 Go to UniProtKB: P54427 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P54427 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | E [auth A], F [auth A], H [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A], D [auth A], G [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALY Query on ALY | A, B | L-PEPTIDE LINKING | C8 H16 N2 O3 |  | LYS |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.152 (Depositor), 0.150 (DCC)
- R-Value Work: 0.125 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.126 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.699 | α = 90 |
| b = 68.856 | β = 90 |
| c = 153.979 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MLPHARE | phasing |
| SBC-Collect | data collection |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-10-14 Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2015-10-14
Type: Initial release - Version 1.1: 2022-03-30
Changes: Author supporting evidence, Data collection, Database references, Derived calculations - Version 1.2: 2024-10-30
Changes: Data collection, Structure summary
