2PVB

PIKE PARVALBUMIN (PI 4.10) AT LOW TEMPERATURE (100K) AND ATOMIC RESOLUTION (0.91 A).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.91 Å
  • R-Value Free: 0.132 
  • R-Value Observed: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core.

Declercq, J.P.Evrard, C.Lamzin, V.Parello, J.

(1999) Protein Sci 8: 2194-2204

  • DOI: 10.1110/ps.8.10.2194
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several crystal structures of parvalbumin (Parv), a typical EF-hand protein, have been reported so far for different species with the best resolution achieving 1.5 A. Using a crystal grown under microgravity conditions, cryotechniques (100 K), and sy ...

    Several crystal structures of parvalbumin (Parv), a typical EF-hand protein, have been reported so far for different species with the best resolution achieving 1.5 A. Using a crystal grown under microgravity conditions, cryotechniques (100 K), and synchrotron radiation, it has now been possible to determine the crystal structure of the fully Ca2+-loaded form of pike (component pI 4.10) Parv.Ca2 at atomic resolution (0.91 A). The availability of such a high quality structure offers the opportunity to contribute to the definition of the validation tools useful for the refinement of protein crystal structures determined to lower resolution. Besides a better definition of most of the elements in the protein three-dimensional structure than in previous studies, the high accuracy thus achieved allows the detection of well-defined alternate conformations, which are observed for 16 residues out of 107 in total. Among them, six occupy an internal position within the hydrophobic core and converge toward two small buried cavities with a total volume of about 60 A3. There is no indication of any water molecule present in these cavities. It is probable that at temperatures of physiological conditions there is a dynamic interconversion between these alternate conformations in an energy-barrier dependent manner. Such motions for which the amplitudes are provided by the present study will be associated with a time-dependent remodeling of the void internal space as part of a slow dynamics regime (millisecond timescales) of the parvalbumin molecule. The relevance of such internal dynamics to function is discussed.


    Related Citations: 
    • A Crystal of a Typical EF-Hand Protein Grown Under Microgravity Diffracts X- Rays Beyond 0.9 A Resolution
      Declercq, J.P., Evrard, C., Carter, D.C., Wright, B.S., Etienne, G., Parello, J.
      (1999) J Cryst Growth 196: 595
    • X-Ray Structure of a New Crystal Form of Pike 4.10 Beta Parvalbumin
      Declercq, J.P., Tinant, B., Parello, J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 165
    • Ionic Interactions with Parvalbumins. Crystal Structure Determination of Pike 4.10 Parvalbumin in Four Different Ionic Environments
      Declercq, J.P., Tinant, B., Parello, J., Rambaud, J.
      (1991) J Mol Biol 220: 1017
    • Crystal Structure Determination and Refinement of Pike 4.10 Parvalbumin (Minor Component from Esox Lucius)
      Declercq, J.P., Tinant, B., Parello, J., Etienne, G., Huber, R.
      (1988) J Mol Biol 202: 349

    Organizational Affiliation

    Université Catholique de Louvain, Unité CPMC, Louvain-la-Neuve, Belgium. declercq@cpmc.ucl.ac.be



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PARVALBUMIN)A108Esox luciusMutation(s): 0 
Find proteins for P02619 (Esox lucius)
Explore P02619 
Go to UniProtKB:  P02619
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download CCD File 
A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.91 Å
  • R-Value Free: 0.132 
  • R-Value Observed: 0.110 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.03α = 90
b = 49.81β = 90
c = 34.57γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-07
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance