6YGX | pdb_00006ygx

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

• PDB DOI: https://doi.org/10.2210/pdb6YGX/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., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Co-crystallization, nanoESI-MS and 19F NMR 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.

Macromolecule Content 

• Total Structure Weight: 43.67 kDa 
• Atom Count: 3,101 
• Modeled Residue Count: 352 
• 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
726 (Subject of Investigation/LOI)	C [auth A]	6-azanyl-2-(methylamino)-4-[2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5,6-tetramethoxyoxan-2-yl]ethyl]-1,7-dihydroimidazo[4,5-g]quinazolin-8-one C21 H30 N6 O6 IXUIMEBGCTWFOR-ZIIYPAMZSA-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: 1.35 Å
• R-Value Free:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.083	α = 90
b = 64.98	β = 93.776
c = 71.374	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., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description