5F7R
ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer
- PDB DOI: https://doi.org/10.2210/pdb5F7R/pdb
- Classification: TRANSCRIPTION
- Organism(s): Listeria monocytogenes EGD-e
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2015-12-08 Released: 2016-09-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.200
- R-Value Work: 0.167
- R-Value Observed: 0.168
wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lmo0178 protein | A [auth E], B [auth A] | 404 | Listeria monocytogenes EGD-e | Mutation(s): 0 Gene Names: lmo0178 |  |
UniProt | |||||
Find proteins for Q8YAF1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YAF1 Go to UniProtKB: Q8YAF1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8YAF1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | I [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | G [auth E] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| ZN Query on ZN | E, H [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth E] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.200
- R-Value Work: 0.167
- R-Value Observed: 0.168
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/m35f7r
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.2 | α = 90 |
| b = 95.064 | β = 90 |
| c = 117.144 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2016-09-07 Deposition Author(s): Light, S.H., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2016-09-07
Type: Initial release - Version 1.1: 2016-11-23
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Structure summary
