1CDP

RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.

Swain, A.L.Kretsinger, R.H.Amma, E.L.

(1989) J Biol Chem 264: 16620-16628

  • Primary Citation of Related Structures:  
    1CDP, 5CPV

  • PubMed Abstract: 

    Carp parvalbumin coordinates calcium through one carbonyl oxygen atom and the oxygen-containing side chains of 5 amino acid residues, or 4 residues and a water molecule, in a helix-loop-helix structural motif. Other calcium-binding proteins, including calmodulin and troponin C, also possess this unique calcium-binding design, which is designated EF-hand or calmodulin fold. Parvalbumin has two such sites, labeled CD and EF. Each of the calcium-binding sites of refined structures of proteins belonging to this group has a 7-oxygen coordination sphere except those of the structure of parvalbumin as it was reported in 1975. This structure had been refined at 1.9 A using difference Fourier techniques on film data. The CD site appeared to be 6-coordinate and the EF site 8-coordinate. Results of NMR experiments using 113Cd-substituted parvalbumin, however, indicate that the sites are similar to one another with coordination number greater than 6. To resolve the inconsistency between crystallographic and NMR results, 1.6 A area detector data was collected for native and cadmium-substituted parvalbumin; the structures have been refined to R factors of 18.7% and 16.4%, respectively, with acceptable geometry and low errors in atomic coordinates. Differences between the parvalbumin structure described in 1975 and the present structure are addressed, including the discovery of 7-coordination for both the CD and EF sites.


  • Organizational Affiliation

    Department of Chemistry, University of South Carolina, Columbia 29208.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CADMIUM-SUBSTITUTED CALCIUM-BINDING PARVALBUMIN B109Cyprinus carpioMutation(s): 0 
UniProt
Find proteins for P02618 (Cyprinus carpio)
Explore P02618 
Go to UniProtKB:  P02618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02618
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.44α = 90
b = 60.46β = 94.8
c = 54.12γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary