4PDQ | pdb_00004pdq

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog

• PDB DOI: https://doi.org/10.2210/pdb4PDQ/pdb
• NAKB: 4PDQ

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


• Deposited: 2014-04-21 Released: 2015-01-07 
• Deposition Author(s): Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Feeney, L.A., Armstrong, E.S., Kondo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs

Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Matias, R.D., Serio, A., Kondo, J.

(2014) Chem Sci 5: 4621-4632

• DOI: https://doi.org/10.1039/C4SC01626B

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 15.51 kDa 
• Atom Count: 1,026 
• Modeled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-*UP*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
NMZ	D [auth B]	(2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy }-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide C27 H52 F N7 O14 VWXJAOATJPQONW-MKAHEPKYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.657	α = 90
b = 103.657	β = 90
c = 44.572	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	phasing
PHENIX	model building
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-07 
Deposition Author(s): Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Feeney, L.A., Armstrong, E.S., Kondo, J.

Revision History  

• Version 1.0: 2015-01-07
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Structure summary