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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.70048
Primary Citation of 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.

Organizational Affiliation

P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Changa, Anand, Gujarat, India.

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

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(by identity cutoff) | 3D Structure

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] 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
UniProt
Find proteins for P50033 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P50033 Go to UniProtKB: P50033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50033
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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] 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
UniProt
Find proteins for A0A6M8B984 (Thermoleptolyngbya sichuanensis A183) Explore A0A6M8B984 Go to UniProtKB: A0A6M8B984
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6M8B984
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth L] SDF format, chain X [auth L] SDF format, chain W [auth J] SDF format, chain V [auth J] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth H] SDF format, chain P [auth H] SDF format, chain O [auth K] SDF format, chain N [auth F] SDF format, chain M [auth F] SDF format, chain FA [auth I] SDF format, chain EA [auth G] SDF format, chain DA [auth E] SDF format, chain CA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth L] MOL2 format, chain X [auth L] MOL2 format, chain W [auth J] MOL2 format, chain V [auth J] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth H] MOL2 format, chain O [auth K] MOL2 format, chain N [auth F] MOL2 format, chain M [auth F] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth L] mmCIF format, chain X [auth L] mmCIF format, chain W [auth J] mmCIF format, chain V [auth J] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth H] mmCIF format, chain O [auth K] mmCIF format, chain N [auth F] mmCIF format, chain M [auth F] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth C]	CA [auth C] DA [auth E] EA [auth G] FA [auth I] M [auth F] 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		Interactions Focus chain CA [auth C] Focus chain DA [auth E] Focus chain EA [auth G] Focus chain FA [auth I] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth K] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth E] Focus chain EA [auth G] Focus chain FA [auth I] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth K] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A], BA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	A [auth F] C [auth H] D [auth B] E [auth D] F [auth J] 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