3LN8 | pdb_00003ln8

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 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3LN8

This is version 1.3 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: https://doi.org/10.1042/BJ20100892
  • Primary Citation Related Structures: 
    3LJD, 3LJE, 3LN8

  • 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, 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.


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

Macromolecule Content 

  • Total Structure Weight: 29.67 kDa 
  • Atom Count: 2,518 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYDROLASE
A, B
126Danio rerioMutation(s): 0 
UniProt
Find proteins for E7FH76 (Danio rerio)
Explore E7FH76 
Go to UniProtKB:  E7FH76
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7FH76
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.192 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
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  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Structure summary