9F64 | pdb_00009f64

Crystal structure of thiol peroxidase mutant (C94A) in complex with Metro* (H. pylori

• PDB DOI: https://doi.org/10.2210/pdb9F64/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-04-30 Released: 2025-05-14 
• Deposition Author(s): Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

5-Nitroimidazole ethers boost anti-Helicobacter pylori activity via a dual mode of action and effectively eradicate infections in vivo

Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.93 kDa 
• Atom Count: 1,330 
• Modeled Residue Count: 165 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A	188	Helicobacter pylori	Mutation(s): 1  Gene Names: tpx, HP_0390 EC: 1.11.1.24
UniProt
Find proteins for O25151 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25151  Go to UniProtKB:  O25151

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IAQ (Subject of Investigation/LOI)	B [auth A]	2-(5-azanyl-2-methyl-imidazol-1-yl)ethanol C6 H11 N3 O QIXFXNMDRJRTIJ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.37	α = 90
b = 71.48	β = 115.91
c = 40.77	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1309 - 325871075

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release