4YJJ | pdb_00004yjj

Crystal structure of Phycocyanin from marine cyanobacterium Phormidium rubidum sp. A09DM

• PDB DOI: https://doi.org/10.2210/pdb4YJJ/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Phormidium
• Mutation(s): No 


• Deposited: 2015-03-03 Released: 2016-03-09 
• Deposition Author(s): Gupta, G.D., Kumar, V., Sonani, R.R., Madamwar, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of Phycocyanin from marine cyanobacterium Phormidium rubidum sp. A09DM

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.48 kDa 
• Atom Count: 5,296 
• Modeled Residue Count: 668 
• Deposited Residue Count: 668 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha Subunit of Cyanobacterial Phycocyanine protein	A, C	162	Phormidium	Mutation(s): 0
UniProt
Find proteins for A0A0B6XLG9 (Phormidium rubidum) Explore A0A0B6XLG9  Go to UniProtKB:  A0A0B6XLG9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta Subunit of Cyanobacterial Phycocyanine protein	B, D	172	Phormidium	Mutation(s): 0
UniProt
Find proteins for A0A0B6XLA1 (Phormidium rubidum) Explore A0A0B6XLA1  Go to UniProtKB:  A0A0B6XLA1

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.354	α = 90
b = 102.354	β = 90
c = 109.021	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Aimless	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Gupta, G.D., Kumar, V., Sonani, R.R., Madamwar, D.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary