5E1P

Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca(2+)-calmodulin.

Lin, J.van den Bedem, H.Brunger, A.T.Wilson, M.A.

(2016) Acta Crystallogr D Struct Biol 72: 83-92

  • DOI: 10.1107/S2059798315021609
  • Primary Citation of Related Structures:  
    5E1K, 5E1N, 5E1P

  • PubMed Abstract: 
  • Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca(2+)-CaM, but no assignment of these features has been made ...

    Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca(2+)-CaM, but no assignment of these features has been made. In addition, Ca(2+)-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca(2+)-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca(2+)-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca(2+)-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca(2+)-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca(2+)-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.


    Organizational Affiliation

    Department of Biochemistry and Redox Biology Center, University of Nebraska, Beadle Center, Lincoln, NE 68588, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CalmodulinA148Paramecium tetraureliaMutation(s): 0 
Gene Names: CAMGSPATT00015825001
Find proteins for P07463 (Paramecium tetraurelia)
Explore P07463 
Go to UniProtKB:  P07463
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.015α = 89.54
b = 29.415β = 86.1
c = 52.761γ = 82.39
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2016-03-16
    Changes: Database references