1BXU

OXIDIZED PLASTOCYANIN FROM SYNECHOCOCCUS SP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure determinations of oxidized and reduced plastocyanin from the cyanobacterium Synechococcus sp. PCC 7942.

Inoue, T.Sugawara, H.Hamanaka, S.Tsukui, H.Suzuki, E.Kohzuma, T.Kai, Y.

(1999) Biochemistry 38: 6063-6069

  • DOI: 10.1021/bi9824442
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of oxidized and reduced plastocyanins from Synechococcus sp. PCC 7942 have been determined at 1.9 and 1.8 A resolution, respectively, at pH 5.0. The protein consists of only 91 amino acid residues, the smallest number known for ...

    The crystal structures of oxidized and reduced plastocyanins from Synechococcus sp. PCC 7942 have been determined at 1.9 and 1.8 A resolution, respectively, at pH 5.0. The protein consists of only 91 amino acid residues, the smallest number known for a plastocyanin, and apparently lacks the mostly conserved acidic patch that is believed to be important for recognition with electron-transfer partners. The protein has two acidic residues, Glu42 and Glu85, around Tyr83, which is thought to be a possible conduit for electrons, but these are neutralized by Arg88 and Lys58. Residue Arg88 interacts with Tyr83 through a pi-pi interaction in which the guanidinium group of the former completely overlaps the aromatic ring of the tyrosine. Reduction of the protein at pH 5.0 causes a lengthening of one Cu-N(His) bond by 0.36 A, despite the small rms deviation of 0.08 A calculated for the backbone atoms. Moreover, significant conformational changes of Arg88 and Lys58, along with the movement of a water molecule adjacent to the OH group of Tyr83, were observed on reduction; the guanidinium group of Arg88 rotates by more than 11 degrees, and the water molecule moves by 0.42 A. The changes around the copper site and the alterations around Tyr83 may be linked to the reduction of the copper.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Plastocyanin from Cyanobacterium Synechococcus Sp. Pcc 7942
      Inoue, T.,Sugawara, H.,Hamanaka, S.,Tsukui, H.,Suzuki, E.,Kohzuma, T.,Kai, Y.
      (1999) Acta Crystallogr.,Sect.D 55: 683


    Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASTOCYANIN
A
91Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: petE
Find proteins for P55020 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  P55020
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 43.100α = 90.00
b = 43.100β = 90.00
c = 56.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance