3V57

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 

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:  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 ob ...

    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 Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin alpha subunit
A, C
164Porphyridium purpureumGene Names: cpeA
Find proteins for P11392 (Porphyridium purpureum)
Go to UniProtKB:  P11392
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin beta subunit
B, D
177Porphyridium purpureumGene Names: cpeB
Find proteins for P11393 (Porphyridium purpureum)
Go to UniProtKB:  P11393
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download SDF File 
Download CCD File 
A, B, C, D
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, D
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 187.110α = 90.00
b = 187.110β = 90.00
c = 59.230γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
ADSCdata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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