2PCY

THE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT 1.8-ANGSTROMS RESOLUTION. THE GEOMETRY OF THE COPPER-BINDING SITE IS CREATED BY THE POLYPEPTIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.160 

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This is version 1.3 of the entry. See complete history. 


Literature

The crystal structure of poplar apoplastocyanin at 1.8-A resolution. The geometry of the copper-binding site is created by the polypeptide

Garrett, T.P., Clingeleffer, D.J., Guss, J.M., Rogers, S.J., Freeman, H.C.

(1984) J Biol Chem 259: 2822-2825

  • DOI: 10.2210/pdb2pcy/pdb
  • Primary Citation of Related Structures:  
    2PCY

  • PubMed Abstract: 

    • The three-dimensional structure of apoplastocyanin from poplar leaves (Populus nigra var. italica) has been determined by x-ray diffraction at 1.8-A resolution. The structure closely resembles that of the holoprotein. In particular, the positions of the copper-binding residues in the apo- and holoproteins differ by only 0 ...

    The three-dimensional structure of apoplastocyanin from poplar leaves (Populus nigra var. italica) has been determined by x-ray diffraction at 1.8-A resolution. The structure closely resembles that of the holoprotein. In particular, the positions of the copper-binding residues in the apo- and holoproteins differ by only 0.1-0.3 A. This indicates that the irregular geometry of the "type 1" copper site is imposed upon the metal atom by the polypeptide moiety. A 180 degrees rotation of one solvent-exposed histidine imidazole ring about C beta-C gamma appears to facilitate access to the copper site. The close structural similarity between apo-, Cu-(II)-, and Cu(I)-plastocyanin was initially demonstrated by means of electron density difference maps. Two series of restrained least squares refinement calculations for apoplastocyanin, originating from different sets of atomic positional parameters, were carried out in parallel. Both refinements converged to the same model which, when fully refined, had a residual R = 0.16. Forty-two water molecules were located during the refinement.

    Related Citations: 
    • Structure of Oxidized Poplar Plastocyanin at 1.6 Angstroms Resolution
      Guss, J.M., Freeman, H.C.
      (1983) J Mol Biol 169: 521
    • X-Ray Crystal Structure Analysis of Plastocyanin at 2.7 Angstroms Resolution
      Colman, P.M., Freeman, H.C., Guss, J.M., Murata, M., Norris, V.A., Ramshaw, J.A.M., Venkatappa, M.P.
      (1978) Nature 272: 319
    Organizational Affiliation: 

    Protein Crystallography Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLASTOCYANINA99Populus nigraMutation(s): 0 
Gene Names: PETE
UniProt
Find proteins for P00299 (Populus nigra)
Explore P00299 
Go to UniProtKB:  P00299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00299
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.53α = 90
b = 46.8β = 90
c = 57.95γ = 90
Software Package:
Software NamePurpose
RESTRAINEDrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1984-02-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other