9G8T | pdb_00009g8t

Crystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb9G8T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-24 Released: 2025-08-06 
• Deposition Author(s): Troilo, F., Giordano, F., Giuffre, A., Giardina, G., Di Matteo, A.
• Funding Organization(s): European Union (EU), Ministero dell Universita e della Ricerca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa

Troilo, F., Giordano, F., Forte, E., Giardina, G., Travaglini-Allocatelli, C., Giuffre, A., Di Matteo, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 33.37 kDa 
• Atom Count: 2,284 
• Modeled Residue Count: 279 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase domain-containing protein	A	296	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA2915
UniProt
Find proteins for Q9HZT2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZT2  Go to UniProtKB:  Q9HZT2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.24	α = 90
b = 77.24	β = 90
c = 83.3	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Troilo, F., Giordano, F., Giuffre, A., Giardina, G., Di Matteo, A.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	PE00000007
Ministero dell Universita e della Ricerca	Italy	20224BYR59
European Union (EU)	European Union	IR0000009

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release