3TD1 | pdb_00003td1

Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticin

• PDB DOI: https://doi.org/10.2210/pdb3TD1/pdb
• NAKB: 3TD1

• Classification: RNA/ANTIBIOTIC
• Mutation(s): No 


• Deposited: 2011-08-10 Released: 2011-12-07 
• Deposition Author(s): Kondo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides

Kondo, J.

(2012) Angew Chem Int Ed Engl 51: 465-468

• PubMed: 22110016 
• DOI: https://doi.org/10.1002/anie.201106084
• Primary Citation of Related Structures:  
  3TD0, 3TD1


• PubMed Abstract: 
  

  Resistance explained: The crystal structures of the ribosomal decoding A site with an A1408G antibiotic-resistance mutation were solved in the presence and absence of the aminoglycoside geneticin (see structure, geneticin carbon framework in yellow). These structures show how bacteria acquire high-level resistance against aminoglycosides by the mutation.

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Organizational Affiliation: 

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.89 kDa 
• Atom Count: 1,216 
• Modelled Residue Count: 45 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')	A, B	23	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GET	C [auth B], D [auth B]	GENETICIN C20 H40 N4 O10 BRZYSWJRSDMWLG-DJWUNRQOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.47	α = 90
b = 88.3	β = 90
c = 46.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
CNS	refinement
d*TREK	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Kondo, J.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description