Download MendeleyStructure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++
Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.(2012) J Biol Chem
4DTF
Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++
- PDB DOI: https://doi.org/10.2210/pdb4DTF/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: 2.12 Å
- R-Value Free: 0.199
- R-Value Work: 0.177
- R-Value Observed: 0.178
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 |  | |
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 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ANP Query on ANP | B [auth A] | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N |  | ||
| SO4 Query on SO4 | F [auth A], G [auth A], H [auth A], I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.12 Å
- R-Value Free: 0.199
- R-Value Work: 0.177
- R-Value Observed: 0.178
- Space Group: P 43 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 128.39 | α = 90 |
| b = 128.39 | β = 90 |
| c = 76.58 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| MOLREP | phasing |
| BUSTER | refinement |
| XDS | data reduction |
| SCALA | data scaling |
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: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
