9BJY

Crystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with TMAO bound

• PDB DOI: https://doi.org/10.2210/pdb9BJY/pdb

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


• Deposited: 2024-04-26 Released: 2024-09-04 
• Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: in silico

Literature

Structure of the RidA protein PA5083 from Pseudomonas aeruginosa with TMAO bound

Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.22 kDa 
• Atom Count: 2,161 
• Modelled Residue Count: 228 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RidA family protein	A [auth B], B [auth A]	115	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA5083
UniProt
Find proteins for Q9HUA0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUA0  Go to UniProtKB:  Q9HUA0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
TMO (Subject of Investigation/LOI)	D [auth B], F [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.28	α = 90
b = 75.28	β = 90
c = 279.505	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release