5MRX | pdb_00005mrx

27-nt SRL with a 5-hydroxymethyl cytidine modification

• PDB DOI: https://doi.org/10.2210/pdb5MRX/pdb
• NAKB: 5MRX

• Classification: RNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-28 Released: 2018-01-17 
• Deposition Author(s): Ennifar, E., Micura, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine

Riml, C., Lusser, A., Ennifar, E., Micura, R.

(2017) J Org Chem 

• DOI: https://doi.org/10.1021/acs.joc.7b01171

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 8.77 kDa 
• Atom Count: 842 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	A	27	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.51	α = 90
b = 29.51	β = 90
c = 76.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Ennifar, E., Micura, R.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2022-03-30
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Refinement description