Download MendeleyStructure and functional characterization of a Vibrio cholerae toxin from the MARTX/VgrG family.
Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.(2012) J Biological Chem
4DTD | pdb_00004dtd
Structure and functional characterization of a Vibrio cholerae toxin from the MARTX/VgrG family.
- PDB DOI: https://doi.org/10.2210/pdb4DTD/pdb
- Classification: TOXIN
- Organism(s): Vibrio cholerae
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2012-02-21 Released: 2012-08-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.213 (Depositor), 0.223 (DCC)
- R-Value Work: 0.187 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.188 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VgrG protein | 396 | Vibrio cholerae | Mutation(s): 0 Gene Names: VC_1416, VgrG1 EC: 6.3.2 |  | |
UniProt | |||||
Find proteins for A0A0H3AIG7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AIG7 Go to UniProtKB: A0A0H3AIG7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0H3AIG7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | B [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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 |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.213 (Depositor), 0.223 (DCC)
- R-Value Work: 0.187 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.188 (Depositor)
Space Group: P 43 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 128.08 | α = 90 |
| b = 128.08 | β = 90 |
| c = 76.52 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
Entry History
Deposition Data
- Released Date: 2012-08-29 Deposition Author(s): Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.
Revision History (Full details and data files)
- Version 1.0: 2012-08-29
Type: Initial release - Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
