8ZN0 | pdb_00008zn0

The Crystal Structure of an Atypical N-methyltransferasea PaOMT9 in P. amurense

• PDB DOI: https://doi.org/10.2210/pdb8ZN0/pdb

• Classification: TRANSFERASE
• Organism(s): Phellodendron amurense
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-25 Released: 2025-05-28 
• Deposition Author(s): Xu, Z.C., Tian, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a N-methylated OMT from P. amurense in complex with SAM and (S)-coclaurine

Xu, Z.C., Tian, Y.

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

Macromolecule Content 

• Total Structure Weight: 81.51 kDa 
• Atom Count: 5,603 
• Modeled Residue Count: 698 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PaOMT9	A, B	359	Phellodendron amurense	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	C [auth A], E [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
A1D8J (Subject of Investigation/LOI)	D [auth A], F [auth B]	(1~{S})-1-[(4-hydroxyphenyl)methyl]-6-methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol C17 H19 N O3 LVVKXRQZSRUVPY-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.346	α = 90
b = 66.346	β = 90
c = 167.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Xu, Z.C., Tian, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release