2BEE | pdb_00002bee

Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site

• PDB DOI: https://doi.org/10.2210/pdb2BEE/pdb
• NAKB: 2BEE

• Classification: RNA/antibiotic
• Organism(s): Streptomyces paromomycinus
• Mutation(s): No 


• Deposited: 2005-10-24 Released: 2005-12-20 
• Deposition Author(s): Francois, B., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.220 (Depositor), 0.217 (DCC) 

Starting Model: experimental

Literature

Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site

Francois, B., Szychowski, J., Adhikari, S.S., Pachamuthu, K., Swayze, E.E., Griffey, R.H., Migawa, M.T., Westhof, E., Hanessian, S.

(2004) Angew Chem Int Ed Engl 43: 6735-6738

• PubMed: 15593140 
• DOI: https://doi.org/10.1002/anie.200462092
• Primary Citation Related Structures: 
  2BE0, 2BEE

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Organizational Affiliation: 
• Institut de biologie moléculaire et cellulaire UPR9002 CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg Cedex, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1,059 
• Modeled Residue Count: 42 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'	A, B	22	Streptomyces paromomycinus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JS4	C [auth A], D [auth B]	(2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-4-(2-(3-AMINOPROPYLAMINO)ETHOXY)-5-((1R,2R,3S,5R,6S)-3,5-DIAM INO-2-((2S,3R,4R,5S,6R)-3-AMINO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-( HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL C28 H57 N7 O14 FJVLHNJZMYGVLT-XXJRHLBLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.220 (Depositor), 0.217 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.171	α = 90
b = 39.171	β = 90
c = 99.027	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Francois, B., Westhof, E.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-03-13
  Changes: Source and taxonomy