1O9M | pdb_00001o9m

The Complex of a novel antibiotic with the Aminoacyl Site of the Bacterial Ribosome Revealed by X-Ray Crystallography.

• PDB DOI: https://doi.org/10.2210/pdb1O9M/pdb
• NAKB: 1O9M

• Classification: ANTIBIOTIC/RNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-17 Released: 2003-03-27 
• Deposition Author(s): Russell, R., Murray, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.298 (Depositor) 
• R-Value Work: 
  0.251 (Depositor) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

The Complex of a Designer Antibiotic with a Model Aminoacyl Site of the 30S Ribosomal Subunit Revealed by X-Ray Crystallography

Russell, R., Murray, J.B., Lentzen, G., Haddad, J., Mobashery, S.

(2003) J Am Chem Soc 125: 3410

• PubMed: 12643685 
• DOI: https://doi.org/10.1021/ja029736h
• Primary Citation Related Structures: 
  1O9M


• PubMed Abstract: 
  

  The ribosome is an important target for aminoglycoside antibiotics; however, the clinical effectiveness of aminoglycosides has diminished due to bacterial resistance mechanisms. Here we report the X-ray structure of a novel synthetic aminoglycoside bound to the A site of the ribosome, its target for manifestation of activity. The structure validates the in silico design paradigms for the antibiotic and reveals the molecular interactions made by this novel antibiotic in prokaryotes.

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Organizational Affiliation: 
• RiboTargets, Granta Park, Cambridge CB1 6GB, United Kingdom.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 14.67 kDa 
• Atom Count: 992 
• Modeled Residue Count: 42 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
EUBACTERIAL A-SITE	A, B	22	Escherichia coli

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDG	C [auth B]	2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose C6 H14 N2 O4 SQTHUUHOUPJYLK-UKFBFLRUSA-N
PA2	D [auth B]	PAROMOMYCIN (RING 2) C6 H14 N2 O2 QOLDZWBHLDQIJR-FSIIMWSLSA-N
P24	E [auth B]	1-(AMINOETHYL)AMINO-4-AMINOBUTANE C6 H17 N3 VRPPEXGZBZBARW-UHFFFAOYSA-N
42B	F [auth B]	4-AMINO-2-HYDROXYBUTANOIC ACID C4 H9 N O3 IVUOMFWNDGNLBJ-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.298 (Depositor) 
• R-Value Work:  0.251 (Depositor) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.8	α = 90
b = 46.55	β = 90
c = 88.81	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-27 
Deposition Author(s): Russell, R., Murray, J.B.

Revision History  

• Version 1.0: 2003-03-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary