9T2W | pdb_00009t2w

YdhG-like domain-containing protein (Frataxin) from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb9T2W/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Listeria monocytogenes 10403S
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-24 Released: 2025-11-19 
• Deposition Author(s): Falb, N., Fink, J., Gabler, T., Hofbauer, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.182 (DCC) 

Starting Model: in silico

Literature

YdhG-like domain-containing protein (Frataxin) from Listeria monocytogenes

Falb, N., Fink, J., Gabler, T., Hofbauer, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.07 kDa 
• Atom Count: 2,152 
• Modeled Residue Count: 243 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YdhG-like domain-containing protein	A, B	123	Listeria monocytogenes 10403S	Mutation(s): 0  Gene Names: LMRG_00080
UniProt
Find proteins for A0A0H3GHN0 (Listeria monocytogenes serotype 1/2a (strain 10403S)) Explore A0A0H3GHN0  Go to UniProtKB:  A0A0H3GHN0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.182 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.974	α = 90
b = 51.296	β = 107.172
c = 60.583	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
gemmi	data extraction
REFMAC	refinement
PHASER	phasing
Coot	model building
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Falb, N., Fink, J., Gabler, T., Hofbauer, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release