7RF0 | pdb_00007rf0

MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND MAGNESIUM

• PDB DOI: https://doi.org/10.2210/pdb7RF0/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacteroides abscessus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-13 Released: 2023-01-18 
• Deposition Author(s): Prucha, G.R., Ismail, M., Suske, A., Das, B., Oz, M., Perez, A., Bolen, R., Jayaraman, S., Stojanoff, V., Halloran, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of divalent Mg+2 dependent Mycobacterium abscessus tRNA (m1 G37) Methyltransferase (TrmD)

Prucha, G.R., Ismail, M., Suske, A., Perez, A., Bolen, R., Jayaraman, S., Stojanoff, V., Halloran, J.

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: 51.8 kDa 
• Atom Count: 3,680 
• Modeled Residue Count: 429 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	233	Mycobacteroides abscessus	Mutation(s): 0  Gene Names: trmD, SAMEA2161603_03547, SAMEA2275821_02238, SAMEA2275847_06627 EC: 2.1.1.228

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.398	α = 90
b = 78.835	β = 90
c = 86.656	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADDREF	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Prucha, G.R., Ismail, M., Suske, A., Das, B., Oz, M., Perez, A., Bolen, R., Jayaraman, S., Stojanoff, V., Halloran, J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	KP1605010
Department of Energy (DOE, United States)	United States	DE-SC0012704
Other private	United States	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection