6ZXV | pdb_00006zxv

Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransferase enzyme bound to sinefungin

• PDB DOI: https://doi.org/10.2210/pdb6ZXV/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-07-30 Released: 2020-09-23 
• Deposition Author(s): Graille, M., Wang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex

Wang, C., Tran, N.V., Jactel, V., Guerineau, V., Graille, M.

(2020) Nucleic Acids Res 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering, gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.88 kDa 
• Atom Count: 5,547 
• Modeled Residue Count: 648 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Guanine(10)-N2)-dimethyltransferase	A, B	340	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: XD40_1676, XD48_1558 EC: 2.1.1.213
UniProt
Find proteins for O29011 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29011  Go to UniProtKB:  O29011

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG (Subject of Investigation/LOI)	C [auth A], G [auth B]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
EDO (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.553	α = 90
b = 74.172	β = 93.51
c = 112.894	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Graille, M., Wang, C.

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references