Download MendeleyCrystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with ferric citrate
Jiang, J.Y., Lu, P., Nagata, K.To be published.
8Y4Y
Crystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with ferric citrate
- PDB DOI: https://doi.org/10.2210/pdb8Y4Y/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Vibrio alginolyticus
- Expression System: Escherichia coli KRX
- Mutation(s): No
- Deposited: 2024-01-31 Released: 2025-02-05
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.51 ?
- R-Value Free: 0.262 (Depositor), 0.263 (DCC)
- R-Value Work: 0.224 (Depositor), 0.224 (DCC)
- R-Value Observed: 0.226 (Depositor)
Starting Model: in silico
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wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| ABC transporter substrate-binding protein | 271 | Vibrio alginolyticus | Mutation(s): 0 Gene Names: HKB16_09180 |  | |
UniProt | |||||
Find proteins for A0A7Y0SGI3 (Vibrio parahaemolyticus) Explore A0A7Y0SGI3 Go to UniProtKB: A0A7Y0SGI3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A7Y0SGI3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FLC Query on FLC | F [auth A], G [auth A] | CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K |  | ||
| PEG Query on PEG | E [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | B [auth A], C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| FE Query on FE | H [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.51 ?
- R-Value Free: 0.262 (Depositor), 0.263 (DCC)
- R-Value Work: 0.224 (Depositor), 0.224 (DCC)
- R-Value Observed: 0.226 (Depositor)
Space Group: I 4 2 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 100.497 | α = 90 |
| b = 100.497 | β = 90 |
| c = 205.983 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| REFMAC | phasing |
| HKL-2000 | data collection |
| XDS | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-02-05 Deposition Author(s): Jiang, J.Y., Lu, P., Nagata, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 19H05771 |
| Japan Society for the Promotion of Science (JSPS) | Japan | JP20K22561 |
| Japan Science and Technology | Japan | JPMJSP2108 |
| Other private | Japan Science Society 2023-4016 |
Revision History (Full details and data files)
- Version 1.0: 2025-02-05
Type: Initial release
