8XEU

Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrichrome bound

PDB DOI: https://doi.org/10.2210/pdb8XEU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptococcus pyogenes SSI-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-13 Released: 2024-10-09
Deposition Author(s): Caaveiro, J.M.M., Fernandez-Perez, J., Tsumoto, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.227
R-Value Work: 0.179

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Conserved binding mechanism for ligand promiscuity in the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes

Fernandez-Perez, J., Caaveiro, J.M.M., Senoo, A., Nakakido, M., De Vega, S., Nakagawa, I., Tsumoto, K.

(null) Structure

DOI: https://doi.org/10.1016/j.str.2024.09.018

Macromolecule Content

Total Structure Weight: 32.59 kDa
Atom Count: 2,496
Modelled Residue Count: 274
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-hydroxamate ABC transporter substrate-binding protein FtsB	A	283	Streptococcus pyogenes SSI-1	Mutation(s): 0 Gene Names: E0F66_02370
UniProt
Find proteins for A0A5S4TPK8 (Streptococcus pyogenes) Explore A0A5S4TPK8 Go to UniProtKB: A0A5S4TPK8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5S4TPK8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FCE (Subject of Investigation/LOI) Query on FCE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FERRICHROME C₂₇ H₄₂ Fe N₉ O₁₂ GGUNGDGGXMHBMJ-OCIDDWSYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.227
R-Value Work: 0.179
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.49	α = 90
b = 62.916	β = 90
c = 67.064	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Caaveiro, J.M.M.

Fernandez-Perez, J.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H02531

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.