1RTB

CRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMPLEX WITH RIBONUCLEASE A

• PDB DOI: https://doi.org/10.2210/pdb1RTB/pdb

• Classification: HYDROLASE(NUCLEIC ACID,RNA)
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1992-08-28 Released: 1993-10-31 
• Deposition Author(s): Birdsall, D.L., McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.228 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A.

Birdsall, D.L., McPherson, A.

(1992) J Biol Chem 267: 22230-22236

• PubMed: 1429575 
• Primary Citation of Related Structures:  
  1RTA, 1RTB


• PubMed Abstract: 
  

  The crystal structure of ribonuclease A with bound thymidylic acid tetramer is reported at 2.5-A resolution. The diffusion of the tetramer into native orthorhombic crystals of the ribonuclease allows for the formation of a structurally stable complex where the single-stranded nucleic acid enters and leaves the enzyme's catalytic region in a persistent 5'-3' direction. The binding of the tetramer to the enzyme's surface is facilitated and mediated by electrostatic interactions between basic protein residues and nucleotide phosphates. Two pyrimidine nucleotides are bound to the enzyme's active site in a manner similar to that observed for other complexes between ribonuclease A and nucleic acid oligomers.

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Organizational Affiliation: 

Division of Biomedical Sciences, Lawrence Livermore National Laboratory, University of California, Livermore 94550.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.71 kDa 
• Atom Count: 951 
• Modelled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.228 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.9	α = 90
b = 74.9	β = 90
c = 44	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CORELS	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Birdsall, D.L., McPherson, A.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary