Download MendeleyThe crystal structure of an ABC transporter periplasmic binding protein YdcS from Escherichia coli BW25113
Tan, K., SKarina, T., Di Leo, R., Savchenko, A., Joachimiak, A.To be published.
6NLP
The crystal structure of an ABC transporter periplasmic binding protein YdcS from Escherichia coli BW25113
- PDB DOI: https://doi.org/10.2210/pdb6NLP/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Escherichia coli 1-392-07_S4_C3
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2019-01-08 Released: 2019-01-23
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.227
- R-Value Work: 0.181
- R-Value Observed: 0.183
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:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Bacterial extracellular solute-binding family protein | 361 | Escherichia coli 1-392-07_S4_C3 | Mutation(s): 0 Gene Names: AD40_1746 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IMD Query on IMD | C [auth A], H [auth B] | IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O |  | ||
| EDO Query on EDO | D [auth A], E [auth A], F [auth A], G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 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: 1.90 Å
- R-Value Free: 0.227
- R-Value Work: 0.181
- R-Value Observed: 0.183
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 161.895 | α = 90 |
| b = 42.896 | β = 121.96 |
| c = 122.771 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-01-23 Deposition Author(s): Tan, K., SKarina, T., Di Leo, R., Savchenko, A., 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: 2019-01-23
Type: Initial release - Version 1.1: 2019-12-18
Changes: Author supporting evidence
