3DW6

Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified

• PDB DOI: https://doi.org/10.2210/pdb3DW6/pdb
• NAKB: 3DW6

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-07-21 Released: 2009-03-24 
• Deposition Author(s): Olieric, V., Rieder, U., Lang, K., Serganov, A., Schulze-Briese, C., Micura, R., Dumas, P., Ennifar, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Literature

A fast selenium derivatization strategy for crystallization and phasing of RNA structures.

Olieric, V., Rieder, U., Lang, K., Serganov, A., Schulze-Briese, C., Micura, R., Dumas, P., Ennifar, E.

(2009) RNA 15: 707-715

• PubMed: 19228585 
• DOI: https://doi.org/10.1261/rna.1499309
• Primary Citation of Related Structures:  
  3DVZ, 3DW4, 3DW5, 3DW6, 3DW7


• PubMed Abstract: 
  

  Site-specific 2'-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2'-OCH(3)-modified RNA sequences, prior to the replacement of 2'-OCH(3) groups with their 2'-SeCH(3) counterparts. The method exploits the similar crystallization properties of 2'-OCH(3)- and 2'-SeCH(3)-modified RNAs and has been successfully validated for two test cases. In addition, our data show that 2'-SeCH(3)-modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality.

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Organizational Affiliation: 

Paul Scherrer Institute, Villigen, Switzerland.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.91 kDa 
• Atom Count: 772 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Sarcin/Ricin Domain from E. Coli 23 S rRNA	A	27	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.6	α = 90
b = 29.6	β = 90
c = 76.53	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Olieric, V., Rieder, U., Lang, K., Serganov, A., Schulze-Briese, C., Micura, R., Dumas, P., Ennifar, E.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations