13FI | pdb_000013fi

Adenosine Bound Structure of the Archaeal Dimethyltransferasea TK0807

• PDB DOI: https://doi.org/10.2210/pdb13FI/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-05-04 Released: 2026-10-28 
• Deposition Author(s): Banco, M.T., Tsai, Y., Correa, I.R., Zatopek, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: in silico

Literature

Discovery of Archaeal RNA Methyltransferases Catalyzing N2,7-Dimethylguanosine Modification at Ribosomal A-site

Tsai, Y., Banco, M.T., Wolf, E.J., Mersha, E., Elkins, L., Fluke, K.A., Burkhart, B.W., Dai, N., Kuska, M.S., Zatopek, K.M., Santangelo, T.J., Correa, I.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.22 kDa 
• Atom Count: 3,285 
• Modeled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TK0807	A [auth B]	386	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: TK0807
UniProt
Find proteins for Q5JH73 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JH73  Go to UniProtKB:  Q5JH73

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN (Subject of Investigation/LOI)	C [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
MPD (Subject of Investigation/LOI)	B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL (Subject of Investigation/LOI)	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.495	α = 90
b = 72.877	β = 90
c = 176.719	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Banco, M.T., Tsai, Y., Correa, I.R., Zatopek, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release