3V57

Crystal Structure of the B-phycoerythrin from the red algae Porphyridium Cruentum at pH8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum

Camara-Artigas, A.Bacarizo, J.Andujar-Sanchez, M.Ortiz-Salmeron, E.Mesa-Valle, C.Cuadri, C.Martin-Garcia, J.M.Martinez-Rodriguez, S.Mazzuca-Sobczuk, T.Ibanez, M.J.Allen, J.P.

(2012) FEBS J 279: 3680-3691

  • DOI: 10.1111/j.1742-4658.2012.08730.x
  • Primary Citation of Related Structures:  
    3V57, 3V58

  • PubMed Abstract: 
  • B-phycoerythrin from the red alga Porphyridium cruentum was crystallized using the technique of capillary counter-diffusion. Crystals belonging to the space group R3 with almost identical unit cell constants and diffracting to 1.85 and 1.70 Å were obtained at pH values of 5 and 8, respectively ...

    B-phycoerythrin from the red alga Porphyridium cruentum was crystallized using the technique of capillary counter-diffusion. Crystals belonging to the space group R3 with almost identical unit cell constants and diffracting to 1.85 and 1.70 Å were obtained at pH values of 5 and 8, respectively. The most important difference between structures is the presence of the residue His88α in two different conformations at pH 8. This residue is placed next to the chromophore phycoerythrobilin PEB82α and the new conformation results in the relocation of the hydrogen-bond network and hydration around PEB82α, which probably contributes to the observed pH dependence of the optical spectrum associated with this chromophore. Comparison with the structures of B-phycoerythrin from other red algae shows differences in the conformation of the A-ring of the chromophore PEB139α. This conformational difference in B-phycoerythrin from P. cruentum enables the formation of several hydrogen bonds that connect PEB139α with the chromophore PEB158β at the (αβ)(3) hexamer association interface. The possible influence of these structural differences on the optical spectrum and the ability of the protein to perform energy transfer are discussed, with the two pH-dependent conformations of His88α and PEB82α being proposed as representing critical structural features that are correlated with the pH dependence of the optical spectrum and transient optical states during energy transfer.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycoerythrin alpha subunitA, C164Porphyridium purpureumMutation(s): 0 
Gene Names: cpeA
UniProt
Find proteins for P11392 (Porphyridium purpureum)
Explore P11392 
Go to UniProtKB:  P11392
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phycoerythrin beta subunitB, D177Porphyridium purpureumMutation(s): 0 
Gene Names: cpeB
UniProt
Find proteins for P11393 (Porphyridium purpureum)
Explore P11393 
Go to UniProtKB:  P11393
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , I [auth B] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , O [auth D] , 
E [auth A],  F [auth A],  I [auth B],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  O [auth D],  P [auth D],  Q [auth D]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], L [auth B], R [auth D], S [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, DL-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.11α = 90
b = 187.11β = 90
c = 59.23γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-12-16 
  • Released Date: 2012-10-03 
  • Deposition Author(s): Camara-Artigas, A.

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release