1DY5

Deamidated derivative of bovine pancreatic ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.120 
  • R-Value Observed: 0.101 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Ultrahigh Resolution Crystal Structure of Ribonuclease A Containing an Isoaspartyl Residue: Hydration and Sterochemical Analysis.

Esposito, L.Vitagliano, L.Sica, F.Sorrentino, G.Zagari, A.Mazzarella, L.

(2000) J Mol Biol 297: 713

  • DOI: 10.1006/jmbi.2000.3597
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to ...

    Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.


    Related Citations: 
    • Deamidation in Proteins:The Crystal Structure of Bovine Pancreatic Ribonuclease with an Isoaspartyl Residue at Position 67
      Capasso, S., Di Donato, A., Esposito, L., Sica, F., Sorrentino, G., Vitagliano, L., Zagari, A., Mazzarella, L.
      (1996) J Mol Biol 257: 492

    Organizational Affiliation

    Centro di Studio di Biocristallografia, CNR and Dipartimento di Chimica Università di Napoli "Federico II", Via Mezzocannone 4 I-80134, Napoli, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A, B
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A, B
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.120 
  • R-Value Observed: 0.101 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.314α = 90
b = 37.47β = 94.55
c = 44.915γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Database references, Derived calculations, Non-polymer description, Version format compliance
  • Version 1.2: 2019-04-24
    Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection