Download MendeleyCrystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica
Kim, Y., Chhor, G., Jedrzejczak, R., Winans, S.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)To be published.
5L09
Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica in complex with 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide
- PDB DOI: https://doi.org/10.2210/pdb5L09/pdb
- Classification: TRANSCRIPTION
- Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-07-26 Released: 2016-09-07
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.203
- R-Value Work: 0.169
- R-Value Observed: 0.171
This is version 1.5 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 |
| Quorum-sensing transcriptional activator | 179 | Yersinia enterocolitica subsp. enterocolitica 8081 | Mutation(s): 0 Gene Names: yenR, YE1599 |  | |
UniProt | |||||
Find proteins for A1JMX7 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JMX7 Go to UniProtKB: A1JMX7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1JMX7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 482 Query on 482 | C [auth A], K [auth B] | 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide C10 H15 N O4 YRYOXRMDHALAFL-QMMMGPOBSA-N |  | ||
| SO4 Query on SO4 | D [auth A], L [auth B], M [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | E [auth A] F [auth A] G [auth A] N [auth B] O [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | H [auth A], I [auth A], J [auth B], Q [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-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: 2.00 Å
- R-Value Free: 0.203
- R-Value Work: 0.169
- R-Value Observed: 0.171
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.878 | α = 90 |
| b = 122.775 | β = 90 |
| c = 107.603 | 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: 2016-09-07 Deposition Author(s): Kim, Y., Chhor, G., Jedrzejczak, R., Winans, S.C., Anderson, W.F., 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 | NIAID-DMID-NIHA12011124 |
Revision History (Full details and data files)
- Version 1.0: 2016-09-07
Type: Initial release - Version 1.1: 2017-02-08
Changes: Structure summary - Version 1.2: 2017-09-20
Changes: Author supporting evidence - Version 1.3: 2019-12-11
Changes: Author supporting evidence, Database references, Other, Structure summary - Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description - Version 1.5: 2023-11-15
Changes: Data collection
