4P3S

Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin

• PDB DOI: https://doi.org/10.2210/pdb4P3S/pdb
• NAKB: 4P3S

• Classification: RNA/ANTIBIOTIC
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-03-10 Released: 2016-05-04 
• Deposition Author(s): Kondo, J., Koganei, M.
• Funding Organization(s): MEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 

Literature

Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin

Kondo, J., Koganei, M.

To be published.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 16.31 kDa 
• Atom Count: 1,156 
• Modelled Residue Count: 43 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.09	α = 90
b = 88.83	β = 90
c = 46.61	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SOLVE	phasing
d*TREK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Kondo, J., Koganei, M.

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Funding Organization	Location	Grant Number
MEXT	Japan	23790054

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations