8UZD

The structure of IpCS3, a theobromine methyltransferase from Yerba Mate

• PDB DOI: https://doi.org/10.2210/pdb8UZD/pdb
• Entry: 8UZD supersedes: 8T2G

• Classification: PLANT PROTEIN
• Organism(s): Ilex paraguariensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-14 Released: 2024-01-10 
• Deposition Author(s): Hernandez Garcia, A., Nair, S.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.248 
• R-Value Work: 0.194 

Literature

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Vignale, F.A., Hernandez Garcia, A., Modenutti, C.P., Sosa, E.J., Defelipe, L.A., Oliveira, R.R.M., Nunes, G.L., Acevedo, R.M., Burguener, G.F., Rossi, M., Zapata, P.D., Marti, D.A., Oliveira, G., Smith, M.N., Dubs, N.M., Nair, S.K., Barkman, T.J., Turjanski, A.G.

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)

Macromolecule Content

• Total Structure Weight: 82.79 kDa 
• Atom Count: 5,340 
• Modelled Residue Count: 663 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IpCS3	A, B	366	Ilex paraguariensis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CFF (Subject of Investigation/LOI)	D [auth A], F [auth B]	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.248 
• R-Value Work: 0.194 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.675	α = 90
b = 82.675	β = 90
c = 226.088	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Hernandez Garcia, A., Nair, S.K.
• This entry supersedes: 8T2G

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM079038

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory