1T0E | pdb_00001t0e

Crystal Structure of 2-aminopurine labelled bacterial decoding site RNA

• PDB DOI: https://doi.org/10.2210/pdb1T0E/pdb
• NAKB: 1T0E

• Classification: RNA
• Mutation(s): No 


• Deposited: 2004-04-08 Released: 2004-06-15 
• Deposition Author(s): Shandrick, S., Zhao, Q., Han, Q., Ayida, B.K., Takahashi, M., Winters, G.C., Simonsen, K.B., Vourloumis, D., Hermann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Monitoring molecular recognition of the ribosomal decoding site.

Shandrick, S., Zhao, Q., Han, Q., Ayida, B.K., Takahashi, M., Winters, G.C., Simonsen, K.B., Vourloumis, D., Hermann, T.

(2004) Angew Chem Int Ed Engl 43: 3177-3182

• PubMed: 15199571 
• DOI: https://doi.org/10.1002/anie.200454217
• Primary Citation of Related Structures:  
  1T0D, 1T0E

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Organizational Affiliation: 
• Department of Structural Chemistry, Anadys Pharmaceuticals, Inc 9050 Camino Santa Fe, San Diego, CA 92121, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.41 kDa 
• Atom Count: 949 
• Modeled Residue Count: 35 
• Deposited Residue Count: 35 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*CP*GP*G)-3'	A	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'	B [auth C]	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C, D [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.04	α = 90
b = 32.95	β = 90
c = 92.69	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Shandrick, S., Zhao, Q., Han, Q., Ayida, B.K., Takahashi, M., Winters, G.C., Simonsen, K.B., Vourloumis, D., Hermann, T.

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description