Download MendeleyCrystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal
Tomoo, K., Miyamoto, K.To be published.
7W8F
Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal
- PDB DOI: https://doi.org/10.2210/pdb7W8F/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Vibrio vulnificus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2021-12-07 Released: 2022-12-07
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.219
- R-Value Work: 0.176
This is version 1.1 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 |
| Putative periplasm binding protein | 280 | Vibrio vulnificus | Mutation(s): 0 Gene Names: fhuD |  | |
UniProt | |||||
Find proteins for Q845T3 (Vibrio vulnificus) Explore Q845T3 Go to UniProtKB: Q845T3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q845T3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| KTY (Subject of Investigation/LOI) Query on KTY | B [auth A] | desferrioxamine B C25 H48 N6 O8 UBQYURCVBFRUQT-UHFFFAOYSA-N |  | ||
| FE Query on FE | C [auth A], D [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.219
- R-Value Work: 0.176
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 34.8 | α = 90 |
| b = 57.89 | β = 95.02 |
| c = 62.7 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-12-07 Deposition Author(s): Tomoo, K., Miyamoto, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2022-12-07
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
