8S6L | pdb_00008s6l

AzeD dehydratase of Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb8S6L/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-27 Released: 2025-03-12 
• Deposition Author(s): Calderari, A., Gruez, A., Najah, S., Li, Y., Weissman, K.J.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: in silico

Literature

High resolution structure of azetidomonamide dehydratase

Calderari, A., Gruez, A., Najah, S., Li, Y., Weissman, K.J.

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: SAXS

Macromolecule Content 

• Total Structure Weight: 51.43 kDa 
• Atom Count: 3,761 
• Modeled Residue Count: 433 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthiocerol/phthiodiolone dimycocerosyl transferase	A	461	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA3329 EC: 2.3.1.282
UniProt
Find proteins for Q9HYR6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYR6  Go to UniProtKB:  Q9HYR6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.46	α = 90
b = 67.59	β = 90
c = 116.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Calderari, A., Gruez, A., Najah, S., Li, Y., Weissman, K.J.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE92-0038

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release