1KSO

CRYSTAL STRUCTURE OF APO S100A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.5 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 D Biol Crystallogr 58: 1255-1261

  • DOI: https://doi.org/10.1107/s0907444902008430
  • Primary Citation of Related Structures:  
    1KSO

  • 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 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 Zürich, Switzerland. mittl@bioc.unizh.ch


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S100 CALCIUM-BINDING PROTEIN A3
A, B
101Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P33764 (Homo sapiens)
Explore P33764 
Go to UniProtKB:  P33764
PHAROS:  P33764
GTEx:  ENSG00000188015 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33764
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.769α = 90
b = 58.769β = 90
c = 45.338γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.5: 2024-02-14
    Changes: Advisory, Data collection, Database references