4JAB | pdb_00004jab

U/G Wobble Base Pair in a RNA Duplex

• PDB DOI: https://doi.org/10.2210/pdb4JAB/pdb
• NAKB: 4JAB

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

2-Se Uridine enhanced U/G Wobble Base Pair Discrimination

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

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 5.49 kDa 
• Atom Count: 339 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*GP*UP*AP*UP*AP*C)-3')	A, B	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.681	α = 90
b = 41.681	β = 90
c = 60.014	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	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., Sun, H., Gan, J., Huang, Z.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description