7F86

Crystal structure of Phycoerythrin from Halomicronema Sp. R31DM

PDB DOI: https://doi.org/10.2210/pdb7F86/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Halomicronema sp. R31DM
Mutation(s): No

Deposited: 2021-07-01 Released: 2022-04-13
Deposition Author(s): Patel, S.N., Gupta, G.D., Sonani, R.R., Singh, N.K., Kumar, V., Madamwar, D.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.210
R-Value Work: 0.163
R-Value Observed: 0.165

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 analysis of phycoerythrin from marine cyanobacterium Halomicronema .

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

(2023) J Biomol Struct Dyn 41: 3752-3761

PubMed: 35354393 Search on PubMed
DOI: https://doi.org/10.1080/07391102.2022.2055647
Primary Citation of Related Structures:
7F86

PubMed Abstract:
Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria Halomicronema sp. R31DM is purified and subjected for its structural characterisation by X-ray crystallography in order to understand its light-harvesting characteristics. The crystal structure is solved to a resolution-limit of 2.21 Å with reasonable R-factors values, 0.16/0.21 (R _work/ R _free). PE forms hexamer of hetero-dimers made up of two peptide chains, α- and β-subunits containing 2 and 3 phycoerythrobilin (PEB) chromophores covalently attached to them, respectively. Geometry of five chromophores is analysed along with their relative position within the PE hexamer. Also, their interactions with the surrounding microenvironment are analysed. The plausible energy transfer pathways in hexamer structure have been predicted based on relative position and geometry of chromophores. This structure enriches the structural information of cyanobacterial PE in order to understand its light-harvesting capacity.Communicated by Ramaswamy H. Sarma.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 480.86 kDa
Atom Count: 36,454
Modelled Residue Count: 4,176
Deposited Residue Count: 4,176
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycoerythrin beta subunit	A [auth M] M [auth C] N [auth E] O [auth G] P [auth I] A [auth M], M [auth C], N [auth E], O [auth G], P [auth I], Q [auth K], R [auth N], S [auth P], T [auth R], U [auth T], V, W [auth X]	184	Halomicronema sp. R31DM	Mutation(s): 0
UniProt
Find proteins for A0A1W1IW87 (Halomicronema sp. R31DM) Explore A0A1W1IW87 Go to UniProtKB: A0A1W1IW87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1W1IW87
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycoerythrin alpha subunit	B [auth A] C [auth D] D [auth B] E [auth F] F [auth H] B [auth A], C [auth D], D [auth B], E [auth F], F [auth H], G [auth J], H [auth L], I [auth O], J [auth Q], K [auth U], L [auth W], X [auth Y]	164	Halomicronema sp. R31DM	Mutation(s): 0
UniProt
Find proteins for A0A1W1IVY1 (Halomicronema sp. R31DM) Explore A0A1W1IVY1 Go to UniProtKB: A0A1W1IVY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1W1IVY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEB (Subject of Investigation/LOI) Query on PEB Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain AB [auth E] SDF format, chain AC [auth V] SDF format, chain BA [auth A] SDF format, chain BB [auth E] SDF format, chain BC [auth X] SDF format, chain CA [auth A] SDF format, chain CB [auth E] SDF format, chain CC [auth X] SDF format, chain DA [auth D] SDF format, chain DB [auth G] SDF format, chain DC [auth X] SDF format, chain EA [auth D] SDF format, chain EB [auth G] SDF format, chain EC [auth Y] SDF format, chain FA [auth B] SDF format, chain FB [auth G] SDF format, chain FC [auth Y] SDF format, chain GA [auth B] SDF format, chain GB [auth I] SDF format, chain HA [auth F] SDF format, chain HB [auth I] SDF format, chain IA [auth F] SDF format, chain IB [auth I] SDF format, chain JA [auth H] SDF format, chain JB [auth K] SDF format, chain KA [auth H] SDF format, chain KB [auth K] SDF format, chain LA [auth J] SDF format, chain LB [auth K] SDF format, chain MA [auth J] SDF format, chain MB [auth N] SDF format, chain NA [auth L] SDF format, chain NB [auth N] SDF format, chain OA [auth L] SDF format, chain OB [auth N] SDF format, chain PA [auth O] SDF format, chain PB [auth P] SDF format, chain QA [auth O] SDF format, chain QB [auth P] SDF format, chain RA [auth Q] SDF format, chain RB [auth P] SDF format, chain SA [auth Q] SDF format, chain SB [auth R] SDF format, chain TA [auth U] SDF format, chain TB [auth R] SDF format, chain UA [auth U] SDF format, chain UB [auth R] SDF format, chain VA [auth W] SDF format, chain VB [auth T] SDF format, chain WA [auth W] SDF format, chain WB [auth T] SDF format, chain XA [auth C] SDF format, chain XB [auth T] SDF format, chain Y [auth M] SDF format, chain YA [auth C] SDF format, chain YB [auth V] SDF format, chain Z [auth M] SDF format, chain ZA [auth C] SDF format, chain ZB [auth V] MOL2 format, chain AA [auth M] MOL2 format, chain AB [auth E] MOL2 format, chain AC [auth V] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth E] MOL2 format, chain BC [auth X] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth E] MOL2 format, chain CC [auth X] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth X] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain EC [auth Y] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth Y] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth I] MOL2 format, chain HA [auth F] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain JB [auth K] MOL2 format, chain KA [auth H] MOL2 format, chain KB [auth K] MOL2 format, chain LA [auth J] MOL2 format, chain LB [auth K] MOL2 format, chain MA [auth J] MOL2 format, chain MB [auth N] MOL2 format, chain NA [auth L] MOL2 format, chain NB [auth N] MOL2 format, chain OA [auth L] MOL2 format, chain OB [auth N] MOL2 format, chain PA [auth O] MOL2 format, chain PB [auth P] MOL2 format, chain QA [auth O] MOL2 format, chain QB [auth P] MOL2 format, chain RA [auth Q] MOL2 format, chain RB [auth P] MOL2 format, chain SA [auth Q] MOL2 format, chain SB [auth R] MOL2 format, chain TA [auth U] MOL2 format, chain TB [auth R] MOL2 format, chain UA [auth U] MOL2 format, chain UB [auth R] MOL2 format, chain VA [auth W] MOL2 format, chain VB [auth T] MOL2 format, chain WA [auth W] MOL2 format, chain WB [auth T] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth T] MOL2 format, chain Y [auth M] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth V] MOL2 format, chain Z [auth M] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth V]	AA [auth M] AB [auth E] AC [auth V] BA [auth A] BB [auth E] AA [auth M], AB [auth E], AC [auth V], BA [auth A], BB [auth E], BC [auth X], CA [auth A], CB [auth E], CC [auth X], DA [auth D], DB [auth G], DC [auth X], EA [auth D], EB [auth G], EC [auth Y], FA [auth B], FB [auth G], FC [auth Y], GA [auth B], GB [auth I], HA [auth F], HB [auth I], IA [auth F], IB [auth I], JA [auth H], JB [auth K], KA [auth H], KB [auth K], LA [auth J], LB [auth K], MA [auth J], MB [auth N], NA [auth L], NB [auth N], OA [auth L], OB [auth N], PA [auth O], PB [auth P], QA [auth O], QB [auth P], RA [auth Q], RB [auth P], SA [auth Q], SB [auth R], TA [auth U], TB [auth R], UA [auth U], UB [auth R], VA [auth W], VB [auth T], WA [auth W], WB [auth T], XA [auth C], XB [auth T], Y [auth M], YA [auth C], YB [auth V], Z [auth M], ZA [auth C], ZB [auth V]	PHYCOERYTHROBILIN C₃₃ H₄₀ N₄ O₆ NKCBCVIFPXGHAV-WAVSMFBNSA-N		Interactions Focus chain AA [auth M] Focus chain AB [auth E] Focus chain AC [auth V] Focus chain BA [auth A] Focus chain BB [auth E] Focus chain BC [auth X] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain CC [auth X] Focus chain DA [auth D] Focus chain DB [auth G] Focus chain DC [auth X] Focus chain EA [auth D] Focus chain EB [auth G] Focus chain EC [auth Y] Focus chain FA [auth B] Focus chain FB [auth G] Focus chain FC [auth Y] Focus chain GA [auth B] Focus chain GB [auth I] Focus chain HA [auth F] Focus chain HB [auth I] Focus chain IA [auth F] Focus chain IB [auth I] Focus chain JA [auth H] Focus chain JB [auth K] Focus chain KA [auth H] Focus chain KB [auth K] Focus chain LA [auth J] Focus chain LB [auth K] Focus chain MA [auth J] Focus chain MB [auth N] Focus chain NA [auth L] Focus chain NB [auth N] Focus chain OA [auth L] Focus chain OB [auth N] Focus chain PA [auth O] Focus chain PB [auth P] Focus chain QA [auth O] Focus chain QB [auth P] Focus chain RA [auth Q] Focus chain RB [auth P] Focus chain SA [auth Q] Focus chain SB [auth R] Focus chain TA [auth U] Focus chain TB [auth R] Focus chain UA [auth U] Focus chain UB [auth R] Focus chain VA [auth W] Focus chain VB [auth T] Focus chain WA [auth W] Focus chain WB [auth T] Focus chain XA [auth C] Focus chain XB [auth T] Focus chain Y [auth M] Focus chain YA [auth C] Focus chain YB [auth V] Focus chain Z [auth M] Focus chain ZA [auth C] Focus chain ZB [auth V] Interactions & Density Focus chain AA [auth M] Focus chain AB [auth E] Focus chain AC [auth V] Focus chain BA [auth A] Focus chain BB [auth E] Focus chain BC [auth X] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain CC [auth X] Focus chain DA [auth D] Focus chain DB [auth G] Focus chain DC [auth X] Focus chain EA [auth D] Focus chain EB [auth G] Focus chain EC [auth Y] Focus chain FA [auth B] Focus chain FB [auth G] Focus chain FC [auth Y] Focus chain GA [auth B] Focus chain GB [auth I] Focus chain HA [auth F] Focus chain HB [auth I] Focus chain IA [auth F] Focus chain IB [auth I] Focus chain JA [auth H] Focus chain JB [auth K] Focus chain KA [auth H] Focus chain KB [auth K] Focus chain LA [auth J] Focus chain LB [auth K] Focus chain MA [auth J] Focus chain MB [auth N] Focus chain NA [auth L] Focus chain NB [auth N] Focus chain OA [auth L] Focus chain OB [auth N] Focus chain PA [auth O] Focus chain PB [auth P] Focus chain QA [auth O] Focus chain QB [auth P] Focus chain RA [auth Q] Focus chain RB [auth P] Focus chain SA [auth Q] Focus chain SB [auth R] Focus chain TA [auth U] Focus chain TB [auth R] Focus chain UA [auth U] Focus chain UB [auth R] Focus chain VA [auth W] Focus chain VB [auth T] Focus chain WA [auth W] Focus chain WB [auth T] Focus chain XA [auth C] Focus chain XB [auth T] Focus chain Y [auth M] Focus chain YA [auth C] Focus chain YB [auth V] Focus chain Z [auth M] Focus chain ZA [auth C] Focus chain ZB [auth V]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	A [auth M] M [auth C] N [auth E] O [auth G] P [auth I] A [auth M], M [auth C], N [auth E], O [auth G], P [auth I], Q [auth K], R [auth N], S [auth P], T [auth R], U [auth T], V, W [auth X]	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN