8B4N

X-ray structure of phycoerythrin from Porphyridium cruentum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Inside out Porphyridium cruentum : Beyond the Conventional Biorefinery Concept.

Liberti, D.Imbimbo, P.Giustino, E.D'Elia, L.Ferraro, G.Casillo, A.Illiano, A.Pinto, G.Di Meo, M.C.Alvarez-Rivera, G.Corsaro, M.M.Amoresano, A.Zarrelli, A.Ibanez, E.Merlino, A.Monti, D.M.

(2023) ACS Sustain Chem Eng 11: 381-389

  • DOI: https://doi.org/10.1021/acssuschemeng.2c05869
  • Primary Citation of Related Structures:  
    8B4N

  • PubMed Abstract: 

    Here, an unprecedented biorefinery approach has been designed to recover high-added value bioproducts starting from the culture of Porphyridium cruentum . This unicellular marine red alga can secrete and accumulate high-value compounds that can find applications in a wide variety of industrial fields. 300 ± 67 mg/L of exopolysaccharides were obtained from cell culture medium; phycoerythrin was efficiently extracted (40% of total extract) and isolated by single chromatography, with a purity grade that allowed the crystal structure determination at 1.60 Å; a twofold increase in β-carotene yield was obtained from the residual biomass; the final residual biomass was found to be enriched in saturated fatty acids. Thus, for the first time, a complete exploitation of P. cruentum culture was set up.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, Naples80126, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-phycoerythrin alpha chainA [auth AAA],
D [auth CCC]
164Porphyridium purpureumMutation(s): 0 
UniProt
Find proteins for P11392 (Porphyridium purpureum)
Explore P11392 
Go to UniProtKB:  P11392
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11392
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
B-phycoerythrin beta chainB [auth BBB],
C [auth BbB],
E [auth DDD],
F [auth DbD]
177Porphyridium purpureumMutation(s): 0 
UniProt
Find proteins for P11393 (Porphyridium purpureum)
Explore P11393 
Go to UniProtKB:  P11393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11393
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEB (Subject of Investigation/LOI)
Query on PEB

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth AAA]
J [auth BBB]
L [auth BbB]
M [auth BbB]
G [auth AAA],
H [auth AAA],
J [auth BBB],
L [auth BbB],
M [auth BbB],
N [auth CCC],
O [auth CCC],
P [auth DDD],
R [auth DbD],
S [auth DbD]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
MEN (Subject of Investigation/LOI)
Query on MEN

Download Ideal Coordinates CCD File 
K [auth BbB],
Q [auth DbD]
N-METHYL ASPARAGINE
C5 H10 N2 O3
CFRMVEKWKKDNAH-VKHMYHEASA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth AAA],
T [auth DbD]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.59α = 90
b = 186.59β = 90
c = 59.19γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description