2OIU

L1 Ribozyme Ligase circular adduct

• PDB DOI: https://doi.org/10.2210/pdb2OIU/pdb
• NAKB: 2OIU

• Classification: RNA
• Mutation(s): No 


• Deposited: 2007-01-11 Released: 2007-03-13 
• Deposition Author(s): Robertson, M.P., Scott, W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

The structural basis of ribozyme-catalyzed RNA assembly.

Robertson, M.P., Scott, W.G.

(2007) Science 315: 1549-1553

• PubMed: 17363667 
• DOI: https://doi.org/10.1126/science.1136231
• Primary Citation of Related Structures:  
  2OIU


• PubMed Abstract: 
  

  Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.

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Organizational Affiliation: 

Center for the Molecular Biology of RNA and Department of Chemistry and Biochemistry, Robert L. Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,087 
• Modelled Residue Count: 142 
• Deposited Residue Count: 142 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
L1 Ribozyme RNA Ligase	A [auth P], B [auth Q]	71	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.29	α = 90
b = 100.018	β = 104.42
c = 71.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Robertson, M.P., Scott, W.G.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations