4JAH | pdb_00004jah

Crystal structure of 2-Selenouridine containing RNA

• PDB DOI: https://doi.org/10.2210/pdb4JAH/pdb
• NAKB: 4JAH

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


• Deposited: 2013-02-18 Released: 2014-01-29 
• Deposition Author(s): Jiang, S., Gan, J., Sun, H., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of 2-Selenouridine containing RNA

Jiang, S., Gan, J., Sun, H., Huang, Z.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 15.62 kDa 
• Atom Count: 1,147 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*GP*UP*AP*(RUS)P*AP*C)-3')	A, B, C [auth D], D [auth E], E [auth C], F	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	G [auth A], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.444	α = 90
b = 46.444	β = 90
c = 120.612	γ = 120

Software Package:

Software Name	Purpose
Web-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Jiang, S., Gan, J., Sun, H., Huang, Z.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description