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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7Y0SGI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
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 ( 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

View Full Validation Report

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