8B4N | pdb_00008b4n

X-ray structure of phycoerythrin from Porphyridium cruentum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.226 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 78.9 kDa 
  • Atom Count: 5,990 
  • Modeled Residue Count: 682 
  • Deposited Residue Count: 682 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
B-phycoerythrin alpha chainA [auth AAA],
C [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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
B-phycoerythrin beta chainB [auth BBB],
D [auth DDD]
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEB
(Subject of Investigation/LOI)

Query on PEB



Download:Ideal Coordinates CCD File
E [auth AAA]
F [auth AAA]
H [auth BBB]
I [auth BBB]
J [auth BBB]
E [auth AAA],
F [auth AAA],
H [auth BBB],
I [auth BBB],
J [auth BBB],
K [auth CCC],
L [auth CCC],
M [auth DDD],
N [auth DDD],
O [auth DDD]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth AAA],
P [auth DDD]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B [auth BBB],
D [auth DDD]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.226 (DCC) 
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

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Ligand Structure Quality Assessment 


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
  • Version 2.0: 2024-07-24
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Other, Polymer sequence, Source and taxonomy, Structure summary