2BV8

The crystal structure of Phycocyanin from Gracilaria chilensis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The Structure at 2 A Resolution of Phycocyanin from Gracilaria Chilensis and the Energy Transfer Network in a Pc-Pc Complex.

Contreras-Martel, C.Matamala, A.Bruna, C.Poo-Caama, G.Almonacid, D.Figueroa, M.Martinez-Oyanedel, J.Bunster, M.

(2007) Biophys Chem 125: 388

  • DOI: https://doi.org/10.1016/j.bpc.2006.09.014
  • Primary Citation of Related Structures:  
    2BV8

  • PubMed Abstract: 

    Phycocyanin is a phycobiliprotein involved in light harvesting and conduction of light to the reaction centers in cyanobacteria and red algae. The structure of C-phycocyanin from Gracilaria chilensis was solved by X-ray crystallography at 2.0 A resolution in space group P2(1). An interaction model between two PC heterohexamers was built, followed by molecular dynamic refinement. The best model showed an inter-hexamer rotation of 23 degrees . The coordinates of a PC heterohexamer (alphabeta)(6) and of the PC-PC complex were used to perform energy transfer calculations between chromophores pairs using the fluorescence resonance energy transfer approach (FRET). Two main intra PC ((I)beta(3)(82)-->(I)alpha(1)(84)-->(I)alpha(5)(84)-->(I)beta(6)(82) and (I)beta(3)(153)-->(I)beta(5)(153)) and two main inter PC ((I)beta(6)(82)-->(II)beta(3)(82) and (I)beta(5)(153)-->(II)beta(3)(153)) pathways were proposed based on the values of the energy transfer constants calculated for all the chromophore pairs in the hexamer and in the complex.


  • Organizational Affiliation

    Institut de Biologie Structurale, CEA-CNRS-UJF, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-PHYCOCYANIN ALPHA SUBUNIT162Agarophyton chilenseMutation(s): 0 
UniProt
Find proteins for Q6B8L6 (Gracilaria tenuistipitata var. liui)
Explore Q6B8L6 
Go to UniProtKB:  Q6B8L6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B8L6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-PHYCOCYANIN BETA SUBUNIT172Agarophyton chilenseMutation(s): 0 
UniProt
Find proteins for Q6B8L7 (Gracilaria tenuistipitata var. liui)
Explore Q6B8L7 
Go to UniProtKB:  Q6B8L7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B8L7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download Ideal Coordinates CCD File 
O [auth B]PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
CYC
Query on CYC

Download Ideal Coordinates CCD File 
AA [auth N]
BA [auth O]
CA [auth P]
DA [auth P]
M [auth A]
AA [auth N],
BA [auth O],
CA [auth P],
DA [auth P],
M [auth A],
N [auth B],
P [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth F],
U [auth F],
V [auth K],
W [auth L],
X [auth L],
Y [auth M],
Z [auth N]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B
D
F
H [auth L]
J [auth N]
B,
D,
F,
H [auth L],
J [auth N],
L [auth P]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.985α = 90
b = 151.803β = 117.45
c = 101.548γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description