3A1R

Neutron crystal structure analysis of bovine pancreatic ribonuclease A


Experimental Data Snapshot

    wwPDB Validation   3D Report Full Report


    This is version 1.4 of the entry. See complete history


    Literature

    A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution

    Yagi, D.Yamada, T.Kurihara, K.Ohnishi, Y.Yamashita, M.Tamada, T.Tanaka, I.Kuroki, R.Niimura, N.

    (2009) Acta Crystallogr D Biol Crystallogr 65: 892-899

    • DOI: 10.1107/S0907444909018885
    • Primary Citation of Related Structures:  
      3A1R

    • PubMed Abstract: 
    • A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 A resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A ...

      A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 A resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 A resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences in hydrogen-bond strengths for the alpha-helices and beta-sheets were inferred from determination of the hydrogen-bond lengths and the H/D-exchange ratios of the backbone amide H atoms. The correlation between the B factors and hydrogen-bond lengths of the hydration water molecules was also determined.


      Organizational Affiliation

      Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan.



    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  3D Structure
    Entity ID: 1
    MoleculeChainsSequence LengthOrganismDetailsImage
    Ribonuclease pancreaticA124Bos taurusMutation(s): 0 
    Gene Names: RNASE1RNS1
    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
    Entity Groups  
    Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
    UniProt GroupP61823
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 30.38α = 90
    b = 38.558β = 105.78
    c = 53.398γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2009-09-01
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Non-polymer description, Version format compliance
    • Version 1.2: 2018-03-07
      Changes: Data collection
    • Version 1.3: 2018-06-13
      Changes: Data collection
    • Version 1.4: 2018-07-18
      Changes: Data collection