4P3U | pdb_00004p3u

Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)

• PDB DOI: https://doi.org/10.2210/pdb4P3U/pdb
• NAKB: 4P3U

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


• Deposited: 2014-03-10 Released: 2016-05-04 
• Deposition Author(s): Kondo, J., Koganei, M.
• Funding Organization(s): MEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.302 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.295 (Depositor), 0.260 (DCC) 

Literature

Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)

Kondo, J., Koganei, M.

To be published.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.65 kDa 
• Atom Count: 1,846 
• Modeled Residue Count: 86 
• Deposited Residue Count: 92 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'	A, B, C, D	23	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.302 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.295 (Depositor), 0.260 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.38	α = 90
b = 32.73	β = 117.06
c = 80.99	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
d*TREK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Kondo, J., Koganei, M.

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Funding Organization	Location	Grant Number
MEXT	Japan	23790054

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations