Download MendeleyThe crystal structure of a class D beta-lactamase from Agrobacterium tumefaciens
Tan, K., Wu, R., Endres, M., Joachimiak, A.To be published.
6V6N
The crystal structure of a class D beta-lactamase from Agrobacterium tumefaciens
- PDB DOI: https://doi.org/10.2210/pdb6V6N/pdb
- Classification: HYDROLASE
- Organism(s): Agrobacterium tumefaciens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2019-12-05 Released: 2019-12-18
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.248
- R-Value Work: 0.211
- R-Value Observed: 0.213
wwPDB Validation 3D Report Full Report
This is version 1.0 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 | 251 | Agrobacterium tumefaciens | Mutation(s): 1 Gene Names: oxa, AtA6_05530, BV900_07365 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for A0A1V2APZ1 (Rhizobium radiobacter) Explore A0A1V2APZ1 Go to UniProtKB: A0A1V2APZ1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A1V2APZ1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | I [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | E [auth A], G [auth B], H [auth C], J [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | F [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KCX Query on KCX | A, B, C, D | L-PEPTIDE LINKING | C7 H14 N2 O4 |  | LYS |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.248
- R-Value Work: 0.211
- R-Value Observed: 0.213
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.119 | α = 90 |
| b = 101.655 | β = 97.841 |
| c = 108.142 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-12-18 Deposition Author(s): Tan, K., 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 | HHSN272201700060C |
Revision History (Full details and data files)
- Version 1.0: 2019-12-18
Type: Initial release
