3TD1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243
R-Value Work: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

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. j.kondo@sophia.ac.jp

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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(UPUPGPCPGPUPCPGPCPGP(5BU)PCPGPAPCPGPAPAPGPUPCPGP*C)-3')	A, B	23	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GET Query on GET Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	GENETICIN C₂₀ H₄₀ N₄ O₁₀ BRZYSWJRSDMWLG-DJWUNRQOSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243
R-Value Work: 0.196
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Kondo, J.

Revision History (Full details and data files)

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