5V0K | pdb_00005v0k

RNA duplex with 2-MeImpG analogue bound-3 binding sites

• PDB DOI: https://doi.org/10.2210/pdb5V0K/pdb
• NAKB: 5V0K

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


• Deposited: 2017-02-28 Released: 2017-03-08 
• Deposition Author(s): Zhang, W., Tam, C.P., Szostak, J.W.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

RNA duplex with 2-MeImpG analogue bound-3 binding sites

Zhang, W., Tam, C.P., Szostak, J.W.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 5.05 kDa 
• Atom Count: 366 
• Modeled Residue Count: 13 
• Deposited Residue Count: 13 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3')	A	13	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8OS	B [auth A], C [auth A]	5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine C14 H18 N7 O7 P MUFMHNGPMISZRD-HTVVRFAVSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.229	α = 90
b = 42.229	β = 90
c = 40.098	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Zhang, W., Tam, C.P., Szostak, J.W.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description