1JBO

The 1.45A Three-Dimensional Structure of c-Phycocyanin from the Thermophylic Cyanobacterium Synechococcus elongatus

• PDB DOI: https://doi.org/10.2210/pdb1JBO/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Synechococcus elongatus
• Mutation(s): Yes 


• Deposited: 2002-05-02 Released: 2003-03-18 
• Deposition Author(s): Nield, J., Rizkallah, P.J., Barber, J., Chayen, N.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.188 
• R-Value Work: 0.146 

Literature

The 1.45A three-dimensional structure of C-phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus

Nield, J., Rizkallah, P.J., Barber, J., Chayen, N.E.

(2003) J Struct Biol 141: 149-155

• PubMed: 12615541 
• DOI: https://doi.org/10.1016/s1047-8477(02)00609-3
• Primary Citation of Related Structures:  
  1JBO


• PubMed Abstract: 
  

  The conversion of solar radiation to chemical energy by photosynthetic organisms provides the primary driving force for life on earth. Light energy is captured by a variety of pigments, usually bound to proteins, which vary with different types of organisms. We report here the 1.45 A resolution three-dimensional structure of one such pigment protein, C-phycocyanin, from Synechococcus elongatus. The structure is at the highest resolution achieved for any such phycobiliprotein. This level of resolution was made possible by implementing a novel crystallization method whereby nucleation is decoupled from subsequent growth, by incubating crystallizing drops for 7h under nucleation conditions and then transferring them to metastable conditions for growth. This is done without touching the crystallization drops throughout the process.

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Organizational Affiliation: 

Wolfson Laboratories, Department of Biological Sciences, Imperial College London SW7 2AZ, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 37.44 kDa 
• Atom Count: 3,153 
• Modelled Residue Count: 334 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Phycocyanin alpha chain	A	162	Synechococcus elongatus	Mutation(s): 0
UniProt
Find proteins for P50032 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P50032  Go to UniProtKB:  P50032

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Phycocyanin beta chain	B	172	Synechococcus elongatus	Mutation(s): 1
UniProt
Find proteins for P50033 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P50033  Go to UniProtKB:  P50033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	C [auth A], D [auth B], E [auth B]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.188 
• R-Value Work: 0.146 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.995	α = 90
b = 187.995	β = 90
c = 60.542	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-18 
Deposition Author(s): Nield, J., Rizkallah, P.J., Barber, J., Chayen, N.E.

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description