1U9S | pdb_00001u9s

Crystal structure of the specificity domain of Ribonuclease P of the A-type

• PDB DOI: https://doi.org/10.2210/pdb1U9S/pdb
• NAKB: 1U9S

• Classification: RNA
• Mutation(s): No 


• Deposited: 2004-08-10 Released: 2004-10-26 
• Deposition Author(s): Krasilnikov, A.S., Xiao, Y., Pan, T., Mondragon, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Basis for structural diversity in homologous RNAs.

Krasilnikov, A.S., Xiao, Y., Pan, T., Mondragon, A.

(2004) Science 306: 104-107

• PubMed: 15459389 
• DOI: https://doi.org/10.1126/science.1101489
• Primary Citation Related Structures: 
  1U9S


• PubMed Abstract: 
  

  Large RNA molecules, such as ribozymes, fold with well-defined tertiary structures that are important for their activity. There are many instances of ribozymes with identical function but differences in their secondary structures, suggesting alternative tertiary folds. Here, we report a crystal structure of the 161-nucleotide specificity domain of an A-type ribonuclease P that differs in secondary and tertiary structure from the specificity domain of a B-type molecule. Despite the differences, the cores of the domains have similar three-dimensional structure. Remarkably, the similar geometry of the cores is stabilized by a different set of interactions involving distinct auxiliary elements.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.28 kDa 
• Atom Count: 3,372 
• Modeled Residue Count: 155 
• Deposited Residue Count: 161 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RIBONUCLEASE P	A	161	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	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], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.47	α = 90
b = 120.89	β = 90
c = 133.62	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHARP	phasing
OASIS	model building
CNS	refinement
XDS	data reduction
CCP4	data scaling
OASIS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Krasilnikov, A.S., Xiao, Y., Pan, T., Mondragon, A.

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations