1RWY

CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.162 
  • R-Value Observed: 0.133 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution

Bottoms, C.A.Schuermann, J.P.Agah, S.Henzl, M.T.Tanner, J.J.

(2004) Protein Sci 13: 1724-1734

  • DOI: 10.1110/ps.03571004
  • Primary Citation of Related Structures:  
    1RWY

  • PubMed Abstract: 
  • The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0 ...

    The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and R(free) = 0.162. The average coordinate estimated standard deviations are 0.021 Angstrom and 0.038 Angstrom for backbone atoms and side-chain atoms, respectively. Besides providing a more precise view of the alpha-isoform than previously available, these data permit comparison with the 0.91 Angstrom structure determined for pike beta-parvalbumin. Visualization of the anisotropic displacement parameters as thermal ellipsoids yields insight into the atomic motion within the Ca(2+)-binding sites. The asymmetric unit includes three parvalbumin (PV) molecules. Interestingly, the EF site in one displays uncharacteristic flexibility. The ellipsoids for Asp-92 are particularly large and non-spherical, and the shape of the Ca(2+) ellipsoid implies significant vibrational motion perpendicular to the plane defined by the four y and z ligands. The relative dearth of crystal-packing interactions in this site suggests that the heightened flexibility may be the result of diminished intermolecular contacts. The implication is that, by impeding conformational mobility, crystal-packing forces may cause serious overestimation of EF-hand rigidity. The high quality of the data permitted 11 residues to be modeled in alternative side-chain conformations, including the two core residues, Ile-97 and Leu-105. The discrete disorder observed for Ile-97 may have functional ramifications, providing a mechanism for communicating binding status between the CD and EF binding loops and between the PV metal ion-binding domain and the N-terminal AB region.


    Organizational Affiliation

    Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PARVALBUMIN ALPHA ABC109Rattus norvegicusMutation(s): 0 
Gene Names: PvalbPva
Find proteins for P02625 (Rattus norvegicus)
Explore P02625 
Go to UniProtKB:  P02625
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.162 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.838α = 90
b = 54.708β = 90
c = 153.643γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
SHELXmodel building
HKL-2000data collection
HKL-2000data scaling
CNSphasing
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description