1BYO

WILD-TYPE PLASTOCYANIN FROM SILENE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.189 

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 125: 899-903

  • DOI: 10.1093/oxfordjournals.jbchem.a022366
  • Primary Citation of Related Structures:  
    1BYO, 1BYP

  • 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, respectively ...

    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: 
    • 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 D Biol Crystallogr 53: 129
    • 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 B 48: 790

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PLASTOCYANIN)A, B99Silene latifolia subsp. albaMutation(s): 0 
Gene Names: PETE
UniProt
Find proteins for P07030 (Silene latifolia subsp. alba)
Explore P07030 
Go to UniProtKB:  P07030
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.6α = 90
b = 76.6β = 90
c = 65.5γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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