1KSO

CRYSTAL STRUCTURE OF APO S100A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Metal-free MIRAS phasing: structure of apo-S100A3.

Mittl, P.R.Fritz, G.Sargent, D.F.Richmond, T.J.Heizmann, C.W.Grutter, M.G.

(2002) Acta Crystallogr.,Sect.D 58: 1255-1261


  • PubMed Abstract: 
  • S100 proteins are involved in metal-dependent intracellular signalling. Metal-free S100A3, a cysteine-rich Ca(2+)- and Zn(2+)-binding protein, has been crystallized by vapour diffusion under the strict exclusion of oxygen and in the absence of divale ...

    S100 proteins are involved in metal-dependent intracellular signalling. Metal-free S100A3, a cysteine-rich Ca(2+)- and Zn(2+)-binding protein, has been crystallized by vapour diffusion under the strict exclusion of oxygen and in the absence of divalent metal ions. Metal binding induces large conformational changes, rendering the apo-S100A3 crystals very sensitive to various metal compounds. Therefore, the structure was solved by MIRAS phasing using potassium iodide and xenon derivatives. Iodide replaces a water molecule at the surface of the S100A3 protein, whereas xenon binds in a hydrophobic cavity at the dimer interface. Despite significant non-isomorphism, the combination of both derivatives was sufficient for structure determination. The overall apo-S100A3 structure resembles the structures of metal-free S100B and S100A6 solution structures. In contrast to the NMR structures, the EF-hand loops are well ordered in the apo-S100A3 crystal structure. In the N-terminal pseudo-EF-hand loop a water molecule occupies the position of the Ca(2+) ion. The C-terminal canonical EF-hand loop shows an extended conformation and a different helix arrangement to other S100/metal complex crystal structures.


    Organizational Affiliation

    Institute of Biochemistry, University of Zurich, Winterthurer Strasse 190, 8057 Z├╝rich, Switzerland. mittl@bioc.unizh.ch




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S100 CALCIUM-BINDING PROTEIN A3
A, B
101Homo sapiensGene Names: S100A3 (S100E)
Find proteins for P33764 (Homo sapiens)
Go to Gene View: S100A3
Go to UniProtKB:  P33764
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 58.769α = 90.00
b = 58.769β = 90.00
c = 45.338γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary
  • Version 1.4: 2018-01-31
    Type: Advisory, Experimental preparation