2J96 | pdb_00002j96

The E-configuration of alfa-Phycoerythrocyanin

• PDB DOI: https://doi.org/10.2210/pdb2J96/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Mastigocladus laminosus
• Mutation(s): No 


• Deposited: 2006-11-02 Released: 2007-01-23 
• Deposition Author(s): Schmidt, M., Patel, A., Zhao, Y., Reuter, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.309 (Depositor) 
• R-Value Work: 
  0.235 (Depositor) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the Photochemistry of Alfa-Phycoerythrocyanin

Schmidt, M., Patel, A., Zhao, Y., Reuter, W.

(2007) Biochemistry 46: 416

• PubMed: 17209552 
• DOI: https://doi.org/10.1021/bi061844j
• Primary Citation Related Structures: 
  2J96


• PubMed Abstract: 
  

  Phycobiliproteins and phytochromes are light-harvesting and light-sensing proteins containing linear tetrapyrroles, so-called bile chromophores. The chromophores in certain biliproteins, including the phytochromes, isomerize reversibly from a stable Z-configuration to a stable E-configuration when irradiated with light of the appropriate wavelength. Here, we report the crystal structure of alpha-phycoerythrocyanin with its chromophore in the E-configuration, compare it with the Z-configuration found in trimeric phycoerythrocyanin, and reveal the structural bases of the isomerization. The geometric changes of the chromophore account for the large spectral shift, which characterizes the overall transition. Interactions of the chromophore A and D pyrrole rings with flexible protein moieties are required for the formation and stabilization of the isomers. We predict that the results will hold for all photoactive biliproteins.

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Organizational Affiliation: 
• Physikdepartment E17, Technische Universität München, James Franck Strasse, 85747 Garching, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.34 kDa 
• Atom Count: 2,890 
• Modeled Residue Count: 324 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOERYTHROCYANIN ALPHA CHAIN	A, B	162	Mastigocladus laminosus	Mutation(s): 0
UniProt
Find proteins for P00309 (Mastigocladus laminosus) Explore P00309  Go to UniProtKB:  P00309

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PVN	C [auth A], D [auth B]	PHYCOVIOLOBILIN C33 H40 N4 O6 SYEAKBPGLNVPDH-HVONXEAXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.309 (Depositor) 
• R-Value Work:  0.235 (Depositor) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.808	α = 90
b = 102.598	β = 94.48
c = 32.146	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
BEAST	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Schmidt, M., Patel, A., Zhao, Y., Reuter, W.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Non-polymer description, Other, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary