7W3W

X-ray structure of apo-VmFbpA, a ferric ion-binding protein from Vibrio metschnikovii

PDB DOI: https://doi.org/10.2210/pdb7W3W/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Vibrio metschnikovii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-26 Released: 2021-12-15
Deposition Author(s): Lu, P., Sui, M., Zhang, M., Nagata, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.208
R-Value Work: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake.

Lu, P., Sui, M., Zhang, M., Wang, M., Kamiya, T., Okamoto, K., Itoh, H., Okuda, S., Suzuki, M., Asakura, T., Fujiwara, T., Nagata, K.

(2021) Int J Mol Sci 22

PubMed: 34884815 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/ijms222313010
Primary Citation of Related Structures:
7W3W

PubMed Abstract:
New strategies are needed to combat multidrug-resistant bacteria. The restriction of iron uptake by bacteria is a promising way to inhibit their growth. We aimed to suppress the growth of Vibrio bacterial species by inhibiting their ferric ion-binding protein (FbpA) using food components.

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 33.5 kDa
Atom Count: 2,587
Modelled Residue Count: 309
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-utilization periplasmic protein	A	309	Vibrio metschnikovii	Mutation(s): 0 Gene Names: fbpA, NCTC8563_00091
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.208
R-Value Work: 0.185
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.792	α = 90
b = 90.792	β = 90
c = 149.836	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K22561
Japan Society for the Promotion of Science (JSPS)	Japan	18H02151
Japan Society for the Promotion of Science (JSPS)	Japan	19H03045
Japan Society for the Promotion of Science (JSPS)	Japan	19H05771

Revision History (Full details and data files)

Version 1.0: 2021-12-15
Type: Initial release
Version 1.1: 2022-02-16
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description