8FCI

tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine

• PDB DOI: https://doi.org/10.2210/pdb8FCI/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium avium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-01 Released: 2023-12-13 
• Deposition Author(s): Lavallee, T., Mehta, K., Young, A., Cortes, J., Isaacson, B., Brylewski, J., Schlegel, F., Doti, L., Battaile, K., Stojanoff, V., Perez, A., Bolen, R.
• Funding Organization(s): Brookhaven National Laboratory (BNL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.239 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Literature

tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine

Lavallee, T., Mehta, K., Young, A., Cortes, J., Isaacson, B., Brylewski, J., Schlegel, F., Doti, L., Battaile, K., Stojanoff, V., Perez, A., Bolen, R.

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: homology

Macromolecule Content

• Total Structure Weight: 58.07 kDa 
• Atom Count: 3,243 
• Modelled Residue Count: 394 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	260	Mycobacterium avium	Mutation(s): 0  Gene Names: trmD, MAP_2974c EC: 2.1.1.228
UniProt
Find proteins for Q73VN9 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q73VN9  Go to UniProtKB:  Q73VN9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.239 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.972	α = 90
b = 70.972	β = 90
c = 240.161	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Lavallee, T., Mehta, K., Young, A., Cortes, J., Isaacson, B., Brylewski, J., Schlegel, F., Doti, L., Battaile, K., Stojanoff, V., Perez, A., Bolen, R.

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Funding Organization	Location	Grant Number
Brookhaven National Laboratory (BNL)	United States	DE-SC0012704

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release