1BYO

WILD-TYPE PLASTOCYANIN FROM SILENE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of wild-type and mutant plastocyanins from a higher plant, Silene.

Sugawara, H.Inoue, T.Li, C.Gotowda, M.Hibino, T.Takabe, T.Kai, Y.

(1999) J.Biochem.(Tokyo) 125: 899-903

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plastocyanin functions as an electron carrier between the cytochrome b6f complex and photosystem I. The crystal structures of the wild-type and E43K/D44K double mutant from the higher plant, Silene, have been determined at 2.0 and 1.75 A resolution, ...

    Plastocyanin functions as an electron carrier between the cytochrome b6f complex and photosystem I. The crystal structures of the wild-type and E43K/D44K double mutant from the higher plant, Silene, have been determined at 2.0 and 1.75 A resolution, respectively. The wild-type plastocyanin comprises two monomers per asymmetric unit, one of which shows the unusually great distance between the copper ion and the Ndelta1 atom of H87 because of the hydrogen bond network formation between H87 and symmetry-related G10. The root mean square deviation for Ca atoms between the wild-type and mutant plastocyanins is 0.44 A, however, the electrostatic potential maps of their molecular surfaces are remarkably different. The low electron-transfer rate in the E43K/D44K mutant results from the hindrance of electrostatic interactions, not from the structural change due to the mutation.


    Related Citations: 
    • Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 Angstroms Resolution
      Guss, J.M.,Bartunik, H.D.,Freeman, H.C.
      (1992) Acta Crystallogr., Sect.B 48: 790
    • Crystallization and Preliminary X-Ray Studies of Plastocyanin from Silene Expressed in E. Coli
      Li, C.,Inoue, T.,Gotowda, M.,Hamada, K.,Nishio, N.,Hibino, T.,Takabe, T.,Kai, Y.
      (1997) Acta Crystallogr.,Sect.D 53: 129


    Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PLASTOCYANIN)
A, B
99Silene latifolia subsp. albaMutation(s): 0 
Gene Names: PETE
Find proteins for P07030 (Silene latifolia subsp. alba)
Go to UniProtKB:  P07030
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.600α = 90.00
b = 76.600β = 90.00
c = 65.500γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-15
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance