3NXA

X-ray structure of the apo form of human S100A16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of human S100A16, a low-affinity calcium binder.

Babini, E.Bertini, I.Borsi, V.Calderone, V.Hu, X.Luchinat, C.Parigi, G.

(2011) J Biol Inorg Chem 16: 243-256

  • DOI: 10.1007/s00775-010-0721-3
  • Primary Citation of Related Structures:  
    2L51, 2L50, 3NXA

  • PubMed Abstract: 
  • The homodimeric structure of human S100A16 in the apo state has been obtained both in the solid state and in solution, resulting in good agreement between the structures with the exception of two loop regions. The homodimeric solution structure of human S100A16 was also calculated in the calcium(II)-bound form ...

    The homodimeric structure of human S100A16 in the apo state has been obtained both in the solid state and in solution, resulting in good agreement between the structures with the exception of two loop regions. The homodimeric solution structure of human S100A16 was also calculated in the calcium(II)-bound form. Differently from most S100 proteins, the conformational rearrangement upon calcium binding is minor. This characteristic is likely to be related to the weak binding affinity of the protein for the calcium(II) ions. In turn, this is ascribed to the lack of the glutamate residue at the end of the S100-specific N-domain binding site, which in most S100 proteins provides two important side chain oxygen atoms as calcium(II) ligands. Furthermore, the presence of hydrophobic interactions stronger than for other S100 proteins, present in the closed form of S100A16 between the third and fourth helices, likely make the closed structure of the second EF-hand particularly stable, so even upon calcium(II) binding such a conformation is not disrupted.


    Organizational Affiliation

    Department of Food Science, University of Bologna, Piazza Goidanich 60, 47521, Cesena, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A16 ABCD100Homo sapiensMutation(s): 0 
Gene Names: AAG13S100A16S100F
Find proteins for Q96FQ6 (Homo sapiens)
Explore Q96FQ6 
Go to UniProtKB:  Q96FQ6
NIH Common Fund Data Resources
PHAROS:  Q96FQ6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.252 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.571α = 90
b = 156.571β = 90
c = 38.138γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-07-13 
  • Released Date: 2010-11-03 
  • Deposition Author(s): Calderone, V.

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance