1T0D | pdb_00001t0d

Crystal Structure of 2-aminopurine labelled bacterial decoding site RNA

• PDB DOI: https://doi.org/10.2210/pdb1T0D/pdb
• NAKB: 1T0D

• 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: 2.20 Å
• R-Value Free: 
  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 

Starting Model: in silico

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 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.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.14 kDa 
• Atom Count: 1,613 
• Modeled Residue Count: 66 
• Deposited Residue Count: 66 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'	A, C	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'	B, D	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.64	α = 90
b = 87.32	β = 93.27
c = 32.79	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: 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