7EDL | pdb_00007edl

Crystal structure of the bacterial ribosomal decoding site in complex with G418 and Hg(II)

• PDB DOI: https://doi.org/10.2210/pdb7EDL/pdb
• NAKB: 7EDL

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


• Deposited: 2021-03-16 Released: 2022-03-16 
• Deposition Author(s): Kondo, J., Suzuki, C.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the prokaryotic ribosomal decoding site in complex with G418 and Hg(II)

Kondo, J., Suzuki, C.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 16.14 kDa 
• Atom Count: 1,010 
• Modeled Residue Count: 43 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GET	C [auth A], E [auth B]	GENETICIN C20 H40 N4 O10 BRZYSWJRSDMWLG-DJWUNRQOSA-N
HG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.64	α = 90
b = 97.301	β = 90
c = 47.06	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Kondo, J., Suzuki, C.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description