Download MendeleyCrystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e
Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F.To be published.
4RYK
Crystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e
- PDB DOI: https://doi.org/10.2210/pdb4RYK/pdb
- Classification: DNA BINDING PROTEIN
- Organism(s): Listeria monocytogenes EGD-e
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-12-15 Released: 2015-01-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.199
- R-Value Work: 0.168
- R-Value Observed: 0.169
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Lmo0325 protein | 306 | Listeria monocytogenes EGD-e | Mutation(s): 0 Gene Names: lmo0325 |  | |
UniProt | |||||
Find proteins for Q8YA39 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YA39 Go to UniProtKB: Q8YA39 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8YA39 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TLA Query on TLA | C [auth A] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N |  | ||
| PEG Query on PEG | D [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| 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 |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | B | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.199
- R-Value Work: 0.168
- R-Value Observed: 0.169
- Space Group: I 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.31 | α = 90 |
| b = 103.93 | β = 90 |
| c = 112.81 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Blu-Ice | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2015-01-07 Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2015-01-07
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
