Crystal structure of bovine pancreatic ribonuclease A variant (V47A)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 

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This is version 1.4 of the entry. See complete history


X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability

Kurpiewska, K.Font, J.Ribo, M.Vilanova, M.Lewinski, K.

(2009) Proteins 77: 658-669

  • DOI: https://doi.org/10.1002/prot.22480
  • Primary Citation of Related Structures:  
    3DH5, 3DH6, 3DI7, 3DI8, 3DI9, 3DIB, 3DIC

  • PubMed Abstract: 

    To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule.

  • Organizational Affiliation

    Faculty of Chemistry, Jagiellonian University, Ingardena 3, Kraków 30-060, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic124Bos taurusMutation(s): 1 
Gene Names: RNASE1RNS1
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.147α = 90
b = 64.147β = 90
c = 63.863γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description