8XDS | pdb_00008xds

O-methyltransferase from Lycoris longituba F186Y variant complexed with Mg and SAH

• PDB DOI: https://doi.org/10.2210/pdb8XDS/pdb

• Classification: TRANSFERASE
• Organism(s): Lycoris longituba
• Expression System: Escherichia coli M15
• Mutation(s): Yes 


• Deposited: 2023-12-11 Released: 2024-08-07 
• Deposition Author(s): Saw, Y.Y.H., Nakashima, Y., Morita, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases

Hnin, S.Y.Y., Nakashima, Y., Kodama, T., Morita, H.

(2024) ACS Catal : 11865-11880

• DOI: https://doi.org/10.1021/acscatal.4c03305

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: 55.83 kDa 
• Atom Count: 4,480 
• Modeled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
norbelladine O-methyltransferase	A, B	242	Lycoris longituba	Mutation(s): 1  EC: 2.1.1.336
UniProt
Find proteins for A0A6B9TNK2 (Lycoris longituba) Explore A0A6B9TNK2  Go to UniProtKB:  A0A6B9TNK2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	E [auth A], G [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.49	α = 90
b = 81.229	β = 90
c = 118.468	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Saw, Y.Y.H., Nakashima, Y., Morita, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H02777
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K15303

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release