4RMP

Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM.

Sonani, R.R.Gupta, G.D.Madamwar, D.Kumar, V.

(2015) Plos One 10: e0124580-e0124580

  • DOI: 10.1371/journal.pone.0124580

  • PubMed Abstract: 
  • Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprote ...

    Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.


    Organizational Affiliation

    BRD School of Biosciences, Vadtal Road, Satellite Campus, Sardar Patel University, Vallabh Vidyanagar, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin
A
161Phormidium rubidum A09DMMutation(s): 0 
Gene Names: apcA
Find proteins for A0A078K1U6 (Phormidium rubidum A09DM)
Go to UniProtKB:  A0A078K1U6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin
B
161Phormidium rubidum A09DMMutation(s): 0 
Gene Names: apcB
Find proteins for A0A078K4M9 (Phormidium rubidum A09DM)
Go to UniProtKB:  A0A078K4M9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download SDF File 
Download CCD File 
A, B
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.158 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 101.242α = 90.00
b = 101.242β = 90.00
c = 193.040γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
AutoPROCdata scaling
Aimlessdata scaling
PHENIXrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release