5KVJ | pdb_00005kvj

Crystal structure of the 16-mer doublestranded RNA. Northeast Structural Genomics Consortium (NESG) target RNA1

• PDB DOI: https://doi.org/10.2210/pdb5KVJ/pdb
• NAKB: 5KVJ

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


• Deposited: 2016-07-14 Released: 2016-08-03 
• Deposition Author(s): Vorobiev, S.M., Ma, L.-C., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the 16-mer double stranded RNA.

Vorobiev, S.M., Ma, L.-C., Montelione, G.T.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 10.4 kDa 
• Atom Count: 704 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)-3')	A	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*GP*CP*CP*UP*GP*UP*AP*GP*AP*GP*GP*AP*UP*GP*G)-3')	B	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	C [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.299	α = 90
b = 43.299	β = 90
c = 124.441	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Vorobiev, S.M., Ma, L.-C., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description