8RYD

AzeJ in complex with SAH from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb8RYD/pdb

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


• Deposited: 2024-02-08 Released: 2025-01-01 
• Deposition Author(s): Klaubert, T.J., Gellner, J., Bernard, C., Effert, J., Lombard, C., Kaila, V.R.I., Bode, H.B., Li, Y., Groll, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: in silico

Literature

Molecular basis for azetidine-2-carboxylic acid biosynthesis

Klaubert, T.J., Gellner, J., Bernard, C., Effert, J., Lombard, C., Kaila, V.R.I., Bode, H.B., Li, Y., Groll, M.

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: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 111.79 kDa 
• Atom Count: 7,226 
• Modelled Residue Count: 910 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class I SAM-dependent methyltransferase	A, B, C, D	249	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA3335
UniProt
Find proteins for Q9HYR0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYR0  Go to UniProtKB:  Q9HYR0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.5	α = 90
b = 84.15	β = 90
c = 94.34	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: 2025-01-01 
Deposition Author(s): Klaubert, T.J., Gellner, J., Bernard, C., Effert, J., Lombard, C., Kaila, V.R.I., Bode, H.B., Li, Y., Groll, M.

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

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release