6W15 | pdb_00006w15

Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb6W15/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-03 Released: 2020-05-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis

Dranow, D.M., Bolejack, M.J., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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: 26.44 kDa 
• Atom Count: 1,642 
• Modeled Residue Count: 202 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	234	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: trmD, MSMEI_2377 EC: 2.1.1.228
UniProt
Find proteins for A0QV40 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QV40  Go to UniProtKB:  A0QV40

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w15

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.1	α = 90
b = 59.1	β = 90
c = 114.55	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Data collection, Structure summary