6YYZ

tRNA-Guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

• PDB DOI: https://doi.org/10.2210/pdb6YYZ/pdb

• Classification: TRANSFERASE
• Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-06 Released: 2020-05-13 
• Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.159 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 

Starting Model: experimental

Literature

Co-crystallization, 19F NMR and nanoESI-MS reveal dimer disturbing inhibitors and conformational changes at dimer contacts

Nguyen, A., Heine, A., Klebe, G.

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: 43.63 kDa 
• Atom Count: 3,290 
• Modelled Residue Count: 360 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	388	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 1  Gene Names: tgt, ZMO0363 EC: 2.4.2.29
UniProt
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore P28720  Go to UniProtKB:  P28720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
725 (Subject of Investigation/LOI)	C [auth A]	6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one C19 H26 N6 O5 OMBPYCFBGGXDQG-BNGXUDDSSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FTR	A	L-PEPTIDE LINKING	C11 H11 F N2 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.159 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.723	α = 90
b = 65.036	β = 93.712
c = 71.568	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description