9EGI | pdb_00009egi

Crystal Structure of EgtUC binding domain mutant T274G bound to L-Ergothioneine from S. pneumoniae

PDB DOI: https://doi.org/10.2210/pdb9EGI/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae D39
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-11-21 Released: 2025-11-26
Deposition Author(s): Legg, K.A., Gonzalez-Gutierrez, G., Giedroc, D.P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.201 (Depositor), 0.202 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

C-H...S hydrogen bonds are essential for molecular recognition of ergothioneine by the bacterial ergothioneine transporter EgtUC in Streptococcus pneumoniae.

Legg, K.A., Gonzalez-Gutierrez, G., Edmonds, K.A., Shushkov, P.G., Giedroc, D.P.

To be published.

Macromolecule Content

Total Structure Weight: 62.51 kDa
Atom Count: 4,591
Modeled Residue Count: 547
Deposited Residue Count: 554
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ergothioneine transporter EgtUC	A, B	277	Streptococcus pneumoniae D39	Mutation(s): 1 Gene Names: proWX, SPD_1642
UniProt
Find proteins for A0A0H2ZQB9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZQB9 Go to UniProtKB: A0A0H2ZQB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2ZQB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LW8 (Subject of Investigation/LOI) Query on LW8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium C₉ H₁₆ N₃ O₂ S SSISHJJTAXXQAX-ZETCQYMHSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.201 (Depositor), 0.202 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.153	α = 90
b = 127.313	β = 90
c = 206.655	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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: 2025-11-26

Deposition Author(s):

Gonzalez-Gutierrez, G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118157

Revision History (Full details and data files)

Version 1.0: 2025-11-26
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.