7EDC

Crystal structure of mutant tRNA [Gm18] methyltransferase TrmH (E107G) in complex with S-adenosyl-L-methionine from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb7EDC/pdb

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


• Deposited: 2021-03-15 Released: 2022-03-23 
• Deposition Author(s): Kono, Y., Ito, A., Okamoto, A., Yamagami, R., Hirata, A., Hori, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.202 

Literature

Unique substrate specificity of type II tRNA Gm18 methyltransferase from Escherichia coli

Kono, Y., Ito, A., Okamoto, A., Yamagami, R., Hirata, A., Hori, H.

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: 27.97 kDa 
• Atom Count: 1,927 
• Modelled Residue Count: 236 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanosine(18)-2'-O)-methyltransferase	A	249	Escherichia coli	Mutation(s): 1  Gene Names: trmH EC: 2.1.1.34
UniProt
Find proteins for P0AGJ2 (Escherichia coli (strain K12)) Explore P0AGJ2  Go to UniProtKB:  P0AGJ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
PO4 (Subject of Investigation/LOI)	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.791	α = 90
b = 60.942	β = 122.965
c = 67.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Kono, Y., Ito, A., Okamoto, A., Yamagami, R., Hirata, A., Hori, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06088
Japan Society for the Promotion of Science (JSPS)	Japan	20H03211

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection, Derived calculations