3S49 | pdb_00003s49

RNA crystal structure with 2-Se-uridine modification

• PDB DOI: https://doi.org/10.2210/pdb3S49/pdb
• NAKB: 3S49

• Classification: RNA
• Mutation(s): No 


• Deposited: 2011-05-19 Released: 2011-06-29 
• Deposition Author(s): Sheng, J., Gan, J., Sun, H., Hassan, A.E.H., Jiang, S., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Higher Specificity of RNA Base Pairing with 2-Selenouridine

Sheng, J., Gan, J., Sun, H., Hassan, A.E.H., Jiang, S., Huang, Z.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.14 kDa 
• Atom Count: 1,236 
• Modeled Residue Count: 56 
• Deposited Residue Count: 56 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')	A, B, C, D, E, F, G	8	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.095	α = 90
b = 47.095	β = 90
c = 424.655	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Sheng, J., Gan, J., Sun, H., Hassan, A.E.H., Jiang, S., Huang, Z.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description