Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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This is version 1.4 of the entry. See complete history


The structure and unusual pH dependence of plastocyanin from the fern Dryopteris crassirhizoma. The protonation of an active site histidine is hindered by pi-pi interactions.

Kohzuma, T.Inoue, T.Yoshizaki, F.Sasakawa, Y.Onodera, K.Nagatomo, S.Kitagawa, T.Uzawa, S.Isobe, Y.Sugimura, Y.Gotowda, M.Kai, Y.

(1999) J Biol Chem 274: 11817-11823

  • DOI: https://doi.org/10.1074/jbc.274.17.11817
  • Primary Citation of Related Structures:  
    1KDI, 1KDJ

  • PubMed Abstract: 

    Spectroscopic properties, amino acid sequence, electron transfer kinetics, and crystal structures of the oxidized (at 1.7 A resolution) and reduced form (at 1.8 A resolution) of a novel plastocyanin from the fern Dryopteris crassirhizoma are presented. Kinetic studies show that the reduced form of Dryopteris plastocyanin remains redox-active at low pH, under conditions where the oxidation of the reduced form of other plastocyanins is inhibited by the protonation of a solvent-exposed active site residue, His87 (equivalent to His90 in Dryopteris plastocyanin). The x-ray crystal structure analysis of Dryopteris plastocyanin reveals pi-pi stacking between Phe12 and His90, suggesting that the active site is uniquely protected against inactivation. Like higher plant plastocyanins, Dryopteris plastocyanin has an acidic patch, but this patch is located closer to the solvent-exposed active site His residue, and the total number of acidic residues is smaller. In the reactions of Dryopteris plastocyanin with inorganic redox reagents, the acidic patch (the "remote" site) and the hydrophobic patch surrounding His90 (the "adjacent" site) are equally efficient for electron transfer. These results indicate the significance of the lack of protonation at the active site of Dryopteris plastocyanin, the equivalence of the two electron transfer sites in this protein, and a possibility of obtaining a novel insight into the photosynthetic electron transfer system of the first vascular plant fern, including its molecular evolutionary aspects. This is the first report on the characterization of plastocyanin and the first three-dimensional protein structure from fern plant.

  • Organizational Affiliation

    Faculty of Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan. kohzuma@biomol.sci.ibaraki.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLASTOCYANIN102Adiantum capillus-venerisMutation(s): 0 
Find proteins for Q7SIB8 (Dryopteris crassirhizoma)
Explore Q7SIB8 
Go to UniProtKB:  Q7SIB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIB8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CU

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.118α = 90
b = 73.118β = 90
c = 31.095γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-11
    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: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-04-03
    Changes: Refinement description