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: 1.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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, includin ...

    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.


    Related Citations: 
    • Carp Muscle Calcium-Binding Protein, I.Characterization of the Tryptic Peptides and the Complete Amino Acid Sequence of Component B
      Coffee, C.J.,Bradshaw, R.A.
      (1973) J.Biol.Chem. 248: 3305
    • The Coordination Polyhedron of Ca2+,Cd2+ in Parvalbumin
      Swain, A.L.,Amma, E.L.
      (1989) Inorg.Chim.Acta. 163: 5
    • Carp Muscle Calcium-Binding Protein, III.Phase Refinement Using the Tangent Formula
      Hendrickson, W.A.,Karle, J.
      (1973) J.Biol.Chem. 248: 3327
    • Troponin and Parvalbumin Calcium Binding Regions Predicted in Myosin Light Chain and T4 Lysozyme
      Tufty, R.M.,Kretsinger, R.H.
      (1975) Science 187: 167
    • Structure of a Calcium Binding Carp Myogen
      Nockolds, C.E.,Kretsinger, R.H.,Coffee, C.J.,Bradshaw, R.A.
      (1972) Proc.Natl.Acad.Sci.USA 69: 581
    • Gene Triplication Deduced from the Tertiary Structure of a Muscle Calcium Binding Protein
      Kretsinger, R.H.
      (1972) Nature New Biol. 240: 85
    • Carp Muscle Calcium-Binding Protein, II.Structure Determination and General Description
      Kretsinger, R.H.,Nockolds, C.E.
      (1973) J.Biol.Chem. 248: 3313
    • Calcium Binding Proteins and Natural Membranes
      Kretsinger, R.H.
      (1974) Perspectives in Membrane Biology --: 229
    • The Structure of a Calcium-Binding Protein from Carp Muscle
      Kretsinger, R.H.,Nockolds, C.E.,Coffee, C.J.,Bradshaw, R.A.
      (1972) Cold Spring Harbor Symp.Quant.Biol. 36: 217
    • Gene Duplication in Carp Muscle Calcium Binding Protein
      Mclachlan, A.D.
      (1972) Nature New Biol. 240: 83
    • Terbium Replacement of Calcium in Carp Muscle Calcium-Binding Parvalbumin,an X-Ray Crystallographic Study
      Moews, P.C.,Kretsinger, R.H.
      (1975) J.Mol.Biol. 91: 229
    • The Coordination of Calcium Ions by Carp Muscle Calcium-Binding Proteins A,B,and C
      Coffee, C.J.,Bradshaw, R.A.,Kretsinger, R.H.
      (1974) Adv.Exp.Med.Biol. 48: 211
    • Refinement of the Structure of Carp Muscle Calcium-Binding Parvalbumin by Model Building and Difference Fourier Analysis
      Moews, P.C.,Kretsinger, R.H.
      (1975) J.Mol.Biol. 91: 201


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CADMIUM-SUBSTITUTED CALCIUM-BINDING PARVALBUMIN B
A
109Cyprinus carpioMutation(s): 0 
Find proteins for P02618 (Cyprinus carpio)
Go to UniProtKB:  P02618
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 28.440α = 90.00
b = 60.460β = 94.80
c = 54.120γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other