1KF8

Atomic resolution structure of RNase A at pH 8.8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å

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This is version 1.2 of the entry. See complete history


Literature

Atomic resolution structures of ribonuclease A at six pH values.

Berisio, R.Sica, F.Lamzin, V.S.Wilson, K.S.Zagari, A.Mazzarella, L.

(2002) Acta Crystallogr D Biol Crystallogr 58: 441-450

  • DOI: 10.1107/s0907444901021758
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic r ...

    The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.


    Related Citations: 
    • Protein titration in the crystal state
      Berisio, R., Lamzin, V.S., Sica, F., Wilson, K.S., Zagari, A., Mazzarella, L.
      (1999) J Mol Biol 292: 845

    Organizational Affiliation

    Centro di Studio di Biocristallografia, CNR, Via Mezzocannone 6, I-80134 Napoli, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pancreatic ribonuclease
A
124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.44α = 90
b = 38.38β = 105.74
c = 53.32γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-96refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance