9OZ0 | pdb_00009oz0

Crystal structure of T6SS effector-immunity complex PA3907-PA3908 from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb9OZ0/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-04 Released: 2025-06-18 
• Deposition Author(s): Stogios, P.J., Borek, D., Skarina, T., Osipiuk, J., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.285 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of T6SS effector-immunity complex PA3907-PA3908 from Pseudomonas aeruginosa

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 48.75 kDa 
• Atom Count: 3,310 
• Modeled Residue Count: 404 
• Deposited Residue Count: 417 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity protein 52 domain-containing protein	A	239	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA3908
UniProt
Find proteins for Q9HXA5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXA5  Go to UniProtKB:  Q9HXA5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tox-REase-5 domain-containing protein	B	178	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA3907
UniProt
Find proteins for Q9HXA6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXA6  Go to UniProtKB:  Q9HXA6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.329	α = 90
b = 167.329	β = 90
c = 167.329	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Stogios, P.J., Borek, D., Skarina, T., Osipiuk, J., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272200700058C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release