1KF3

Atomic Resolution Structure of RNase A at pH 5.9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å

wwPDB Validation 3D Report Full Report


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.,Sect.D 58: 441-450

  • Primary Citation of Related Structures:  1KF2, 1KF4, 1KF5, 1KF7, 1KF8
  • Also Cited By: 1YV4, 1YV6, 1YV7

  • 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 taurusGene Names: RNASE1 (RNS1)
EC: 3.1.27.5
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 30.440α = 90.00
b = 38.380β = 105.74
c = 53.320γ = 90.00
Software Package:
Software NamePurpose
SHELXL-96refinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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