7D6W | pdb_00007d6w

Crystal structure of Phycocyanin from Synechococcus sp. R42DM

PDB DOI: https://doi.org/10.2210/pdb7D6W/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Synechococcus sp. R42DM
Mutation(s): No

Deposited: 2020-10-02 Released: 2021-10-06
Deposition Author(s): Patel, S.N., Sonani, R.R., Chaubey, M.G., Singh, N.K., Kumar, V., Madamwar, D.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 ?
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.165 (Depositor), 0.170 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Synechococcus phycocyanin: implications of light-harvesting and antioxidant properties.

Patel, S.N., Sonani, R.R., Chaubey, M.G., Gupta, G.D., Singh, N.K., Kumar, V., Madamwar, D.

(2023) 3 Biotech 13: 247-247

PubMed: 37366498 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13205-023-03665-1
Primary Citation of Related Structures:
7D6W

PubMed Abstract:
Phycobiliproteins is a family of chromophore-containing proteins having light-harvesting and antioxidant capacity. The phycocyanin (PC) is a brilliant blue coloured phycobiliprotein, found in rod structure of phycobilisome and has been widely studied for their therapeutic and fluorescent properties. In the present study, the hexameric assembly structure of phycocyanin (Syn-PC) from Synechococcus Sp. R42DM is characterized by X-ray crystallography to understand its light-harvesting and antioxidant properties. The crystal structure of Syn-PC is solved with 2.15?? resolution and crystallographic R -factors, R _work/ R _free, 0.16/0.21. The hexamer of Syn-PC is formed by heterodimer of two polypeptide chains, namely, α- and β-subunits. The structure is analysed at atomic level to reveal the chromophore microenvironment and possible light energy transfer mechanism in Syn-PC. The chromophore arrangement in hexamer, deviation angle and distance between the chromophore contribute to the energy transfer efficiency of protein. The structural attributes responsible for the antioxidant potential of Syn-PC are recognized and annotated on its 3-dimensional structure. The online version contains supplementary material available at 10.1007/s13205-023-03665-1.

Organizational Affiliation

P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India.

Macromolecule Content

Total Structure Weight: 222.65 kDa
Atom Count: 17,385
Modelled 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 alpha subunit	A, C, E, G, I A, C, E, G, I, K	162	Synechococcus sp. R42DM	Mutation(s): 0
UniProt
Find proteins for P13530 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P13530 Go to UniProtKB: P13530
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13530
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 beta subunit	B, D, F, H, J B, D, F, H, J, L	172	Synechococcus sp. R42DM	Mutation(s): 0
UniProt
Find proteins for P06539 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P06539 Go to UniProtKB: P06539
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth K] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth K] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J]	AA [auth J] BA [auth K] CA [auth L] DA [auth L] M [auth A] AA [auth J], BA [auth K], CA [auth L], DA [auth L], M [auth A], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth F], U [auth F], V [auth G], W [auth H], X [auth H], Y [auth I], Z [auth J]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]