8Z20 | pdb_00008z20

Crystal structure analysis of thermotolerant Oscillatoria Phycocyanin

• PDB DOI: https://doi.org/10.2210/pdb8Z20/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Oscillatoria sp. N9DM
• Mutation(s): No 


• Deposited: 2024-04-12 Released: 2025-04-16 
• Deposition Author(s): Patel, S.N., Sonani, R.R., Gupta, G.D., Upadhyaya, C.T., Sonavane, B.P., Singh, N.K., Kumar, V., Madamwar, D.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structure and stability of phycocyanin from thermotolerant Oscillatoria.

Patel, S.N., Sonani, R.R., Gupta, G.D., Singh, N.K., Upadhyaya, C., Sonavane, B., Amin, S., Kumar, V., Madamwar, D.

(2025) FEBS Lett 599: 1420-1432

• PubMed: 40297916 
• DOI: https://doi.org/10.1002/1873-3468.70048
• Primary Citation Related Structures: 
  8Z20


• PubMed Abstract: 
  

  Phycocyanin (PC), a pigment-protein complex with diverse biotechnological applications, plays a key role in light energy transfer for photosynthesis in cyanobacteria. PC (O-PC) from a thermotolerant cyanobacteria Oscillatoria sp. N09DM exhibits remarkable stability compared to its mesophilic counterparts, making it highly valuable for industrial and medical applications. To understand the basis of its stability, the crystal structure of O-PC is solved and analysed. Structural analysis reveals a key molecular interaction, including hydrogen bonds, salt bridges and hydrophobic interactions, along with amino acid substitutions that provide the thermal stability. Additionally, structural results provide insights into chromophore-protein interactions for understanding O-PC's role in the efficient transfer of light energy.

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Organizational Affiliation: 
• P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Changa, Anand, Gujarat, India.
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India.
Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat, India.
Shree P. M. Patel Institute of Integrated M. Sc. in Biotechnology, Sardar Patel University, Anand, Gujarat, India.

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 Evidence: gel filtration

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: 225.62 kDa 
• Atom Count: 16,110 
• Modeled Residue Count: 2,004 
• Deposited Residue Count: 2,004 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin subunit beta	A [auth F], C [auth H], D [auth B], E [auth D], F [auth J], G [auth L]	172	Oscillatoria sp. N9DM	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin subunit alpha	B [auth K], H [auth A], I [auth C], J [auth E], K [auth G], L [auth I]	162	Oscillatoria sp. N9DM	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	CA [auth C], DA [auth E], EA [auth G], FA [auth I], M [auth F], N [auth F], O [auth K], P [auth H], Q [auth H], R [auth B], S [auth B], T [auth D], U [auth D], V [auth J], W [auth J], X [auth L], Y [auth L], Z [auth A]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N
GOL	AA [auth A], BA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	A [auth F], C [auth H], D [auth B], E [auth D], F [auth J], G [auth L]	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.012	α = 90
b = 153.728	β = 90
c = 207.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Patel, S.N., Sonani, R.R., Gupta, G.D., Upadhyaya, C.T., Sonavane, B.P., Singh, N.K., Kumar, V., Madamwar, D.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	GUJCOST/STI/2021-22/3878

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Database references