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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.222 (Depositor), 0.250 (DCC)
R-Value Work:
0.180 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GHN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.222 (Depositor), 0.250 (DCC)
R-Value Work: 0.180 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.