5E1K

Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia SAD data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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 ...

    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

    Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University and Howard Hughes Medical Institute, Stanford, CA 94305, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.,Department of Biochemistry and Redox Biology Center, University of Nebraska, Beadle Center, Lincoln, NE 68588, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
A
148Paramecium tetraureliaMutation(s): 0 
Gene Names: CAM
Find proteins for P07463 (Paramecium tetraurelia)
Go to UniProtKB:  P07463
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 25.036α = 89.45
b = 29.410β = 86.29
c = 52.794γ = 82.39
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
SHELXLrefinement
SHELXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2016-03-16
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Refinement description