4DS6 | pdb_00004ds6

Crystal structure of a group II intron in the pre-catalytic state

• PDB DOI: https://doi.org/10.2210/pdb4DS6/pdb
• NAKB: 4DS6

• Classification: RNA
• Organism(s): Oceanobacillus iheyensis
• Mutation(s): No 


• Deposited: 2012-02-17 Released: 2012-04-18 
• Deposition Author(s): Chan, R.T., Robart, A.R., Rajashankar, K.R., Pyle, A.M., Toor, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.64 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a group II intron in the pre-catalytic state.

Chan, R.T., Robart, A.R., Rajashankar, K.R., Pyle, A.M., Toor, N.

(2012) Nat Struct Mol Biol 19: 555-557

• PubMed: 22484319 
• DOI: https://doi.org/10.1038/nsmb.2270
• Primary Citation Related Structures: 
  4DS6


• PubMed Abstract: 
  

  Group II introns are self-splicing catalytic RNAs that are thought to be ancestral to the spliceosome. Here we report the 3.65-Å crystal structure of the group II intron from Oceanobacillus iheyensis in the pre-catalytic state. The structure reveals the conformation of the 5' splice site in the catalytic core and represents the first structure of an intron prior to the first step of splicing.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, USA.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 137.29 kDa 
• Atom Count: 8,474 
• Modeled Residue Count: 393 
• Deposited Residue Count: 422 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Mutant Group IIC Intron	A	422	Oceanobacillus iheyensis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.64 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.88	α = 90
b = 95.31	β = 90
c = 226.173	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Chan, R.T., Robart, A.R., Rajashankar, K.R., Pyle, A.M., Toor, N.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2012-06-20
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description