3LN8

The X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.

Pizzo, E.Merlino, A.Turano, M.Russo Krauss, I.Coscia, F.Zanfardino, A.Varcamonti, M.Furia, A.Giancola, C.Mazzarella, L.Sica, F.D'Alessio, G.

(2010) Biochem J 433: 345-355

  • DOI: 10.1042/BJ20100892
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, the ...

    Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.


    Related Citations: 
    • Ribonucleases and angiogenins from fish
      Pizzo, E., Buonanno, P., Di Maro, A., Ponticelli, S., De Falco, S., Quarto, N., Cubellis, M.V., D'Alessio, G.
      (2006) J Biol Chem 281: 27454
    • The success of the RNase scaffold in the advance of biosciences and in evolution
      Pizzo, E., D'Alessio, G.
      (2007) Gene 406: 8

    Organizational Affiliation

    Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROLASE
A, B
126Danio rerioMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.573α = 90
b = 49.183β = 90
c = 110.276γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance