1I7Y

CRYSTAL STRUCTURE OF C-PHYCOCYANIN OF SYNECHOCOCCUS VULCANUS AT 2.5 ANGSTROMS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of c-phycocyanin from the thermophilic cyanobacterium Synechococcus vulcanus at 2.5 A: structural implications for thermal stability in phycobilisome assembly.

Adir, N.Dobrovetsky, Y.Lerner, N.

(2001) J.Mol.Biol. 313: 71-81

  • DOI: 10.1006/jmbi.2001.5030

  • PubMed Abstract: 
  • The crystal structure of the light-harvesting phycobiliprotein, c-phycocyanin from the thermophilic cyanobacterium Synechochoccus vulcanus has been determined by molecular replacement to 2.5 A resolution. The crystal belongs to space group R32 with c ...

    The crystal structure of the light-harvesting phycobiliprotein, c-phycocyanin from the thermophilic cyanobacterium Synechochoccus vulcanus has been determined by molecular replacement to 2.5 A resolution. The crystal belongs to space group R32 with cell parameters a=b=188.43 A, c=61.28 A, alpha=beta=90 degrees, gamma=120 degrees, with one (alphabeta) monomer in the asymmetric unit. The structure has been refined to a crystallographic R factor of 20.2 % (R-free factor is 24.4 %), for all data to 2.5 A. The crystals were grown from phycocyanin (alphabeta)(3) trimers that form (alphabeta)(6) hexamers in the crystals, in a fashion similar to other phycocyanins. Comparison of the primary, tertiary and quaternary structures of the S. vulcanus phycocyanin structure with phycocyanins from both the mesophilic Fremyella diplsiphon and the thermophilic Mastigocladus laminosus were performed. We show that each level of assembly of oligomeric phycocyanin, which leads to the formation of the phycobilisome structure, can be stabilized in thermophilic organisms by amino acid residue substitutions. Each substitution can form additional ionic interactions at critical positions of each association interface. In addition, a significant shift in the position of ring D of the B155 phycocyanobilin cofactor in the S. vulcanus phycocyanin, enables the formation of important polar interactions at both the (alphabeta) monomer and (alphabeta)(6) hexamer association interfaces.


    Organizational Affiliation

    Department of Chemistry and Institute of Catalysis, Science and Technology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel. nadir@tx.technion.ac.il




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-PHYCOCYANIN ALPHA SUBUNIT
A
162Thermosynechococcus vulcanusN/A
Find proteins for Q9AM02 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q9AM02
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-PHYCOCYANIN BETA SUBUNIT
B
172Thermosynechococcus vulcanusN/A
Find proteins for Q71RW8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q71RW8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MEN
Query on MEN

Download SDF File 
Download CCD File 
B
N-METHYL ASPARAGINE
C5 H10 N2 O3
CFRMVEKWKKDNAH-VKHMYHEASA-N
 Ligand Interaction
CYC
Query on CYC

Download SDF File 
Download CCD File 
A, B
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 188.432α = 90.00
b = 188.432β = 90.00
c = 61.276γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance