8Y4Y | pdb_00008y4y

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 
• Deposition Author(s): Jiang, J.Y., Lu, P., Nagata, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.262 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: in silico

Literature

Crystal 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 31.06 kDa 
• Atom Count: 2,195 
• Modeled Residue Count: 271 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein	A	271	Vibrio alginolyticus	Mutation(s): 0  Gene Names: HKB16_09180
UniProt
Find proteins for A0A7Y0SGI3 (Vibrio parahaemolyticus) Explore A0A7Y0SGI3  Go to UniProtKB:  A0A7Y0SGI3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	F [auth A], G [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	H [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.262 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.497	α = 90
b = 100.497	β = 90
c = 205.983	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
REFMAC	phasing
HKL-2000	data collection
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Jiang, J.Y., Lu, P., Nagata, K.

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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  

• Version 1.0: 2025-02-05
  Type: Initial release