6YGV | pdb_00006ygv

tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide

• PDB DOI: https://doi.org/10.2210/pdb6YGV/pdb

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


• Deposited: 2020-03-27 Released: 2020-04-08 
• Deposition Author(s): Nguyen, A., Heyder, L., Heine, A., Diederich, W., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.164 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Ligands disturb dimer contacts

Nguyen, A., Heyder, L., Heine, A., Diederich, W., 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: 43.64 kDa 
• Atom Count: 3,224 
• Modeled Residue Count: 367 
• 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): 5  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OQH (Subject of Investigation/LOI)	H [auth A]	~{N}-ethyl-4-oxidanylidene-4-phenyl-butanamide C12 H15 N O2 DSZHWKIWJYHWTO-UHFFFAOYSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.164 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.824	α = 90
b = 64.911	β = 95.726
c = 71.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Nguyen, A., Heyder, L., Heine, A., Diederich, W., Klebe, G.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-01
  Changes: Advisory, Derived calculations, Structure summary