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Download EndnoteCrystal Structure of the Beta Lactamase Class D YbXI from Nostoc
Kim, Y., Tesar, C., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)To be published.
6NHS
Crystal Structure of the Beta Lactamase Class D YbXI from Nostoc
- DOI: 10.2210/pdb6NHS/pdb
- Classification: HYDROLASE
- Organism(s): Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
- Expression System: Escherichia coli BL21(DE3)
- Deposited: 2018-12-23 Released: 2019-01-16
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2 Å
- R-Value Free: 0.202
- R-Value Work: 0.163
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: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Beta-lactamase | A | 259 | Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) | Mutation(s): 0 |
Find proteins for Q8YU74 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Go to UniProtKB: Q8YU74 | ||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FMT Query on FMT | A | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | A | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| EDO Query on EDO | A | 1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2 Å
- R-Value Free: 0.202
- R-Value Work: 0.163
- Space Group: P 62 2 2
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 116.502 | α = 90.00 |
| b = 116.502 | β = 90.00 |
| c = 74.702 | γ = 120.00 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | refinement |
| HKL-3000 | phasing |
| MLPHARE | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-12-23
- Released Date: 2019-01-16
- Deposition Author(s): Kim, Y., Tesar, C., Endres, M., Babnigg, G., 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 | -- |
