5CX8
Structure of RagB, a major immunodominant virulence factor of Porphyromonas gingivalis.
- PDB DOI: https://doi.org/10.2210/pdb5CX8/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Porphyromonas gingivalis W83
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-07-28 Released: 2015-10-21
- Funding Organization(s): Grants DAVE, European Union, Spanish Ministry for Education, Culture and Sport
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.208
- R-Value Work: 0.178
- R-Value Observed: 0.178
This is version 2.0 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 |
| Lipoprotein RagB | 481 | Porphyromonas gingivalis W83 | Mutation(s): 0 Gene Names: ragB, PG_0186 |  | |
UniProt | |||||
Find proteins for F5H948 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore F5H948 Go to UniProtKB: F5H948 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F5H948 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TG6 Query on TG6 | D [auth A] | 6-O-phosphono-D-tagatose C6 H13 O9 P GSXOAOHZAIYLCY-PBXRRBTRSA-N |  | ||
| RP3 Query on RP3 | I [auth B] | 3-deoxy-5-O-phosphono-beta-D-ribofuranose C5 H11 O7 P OOLHLHJSMUTTHE-VPENINKCSA-N |  | ||
| 3DO Query on 3DO | C [auth A] | 3-deoxy-beta-D-glucopyranose C6 H12 O5 RJDIFQMDPPUATQ-SLPGGIOYSA-N |  | ||
| GOL Query on GOL | E [auth A], F [auth A], J [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | G [auth A], H [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| 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: 2.40 Å
- R-Value Free: 0.208
- R-Value Work: 0.178
- R-Value Observed: 0.178
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.64 | α = 90 |
| b = 184.74 | β = 90 |
| c = 144.31 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| SHELXDE | phasing |
| Coot | model building |
| BUSTER | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-10-21 Deposition Author(s): Goulas, T., Garcia-Ferrer, I., Hutcherson, J.A., Potempa, B.A., Potempa, J., Scott, D.A., Gomis-Ruth, F.X.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Grants DAVE | United States | UMO-2012/04/A/NZ1/00051 |
| Grants DAVE | United States | UMO-2012/05/B/NZ6/00581 |
| Grants DAVE | United States | UMO-2013/08/W/NZ1/00696 |
| European Union | Spain | FP7-PEOPLE-2011-ITN-290246 |
| European Union | Spain | FP7-HEALTH-2012-306029-2 |
| European Union | Spain | BFU2012-32862 |
| Spanish Ministry for Education, Culture and Sport | Spain | JCI-2012-13573 |
| Spanish Ministry for Education, Culture and Sport | Spain | AP2010-3799 |
Revision History (Full details and data files)
- Version 1.0: 2015-10-21
Type: Initial release - Version 1.1: 2016-11-16
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
