1HA7

STRUCTURE OF A LIGHT-HARVESTING PHYCOBILIPROTEIN, C-PHYCOCYANIN FROM SPIRULINA PLATENSIS AT 2.2A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of a Light-Harvesting Protein C-Phycocyanin from Spirulina Platensis

Padyana, A.K., Bhat, V.B., Madyastha, K.M., Rajashankar, K.R., Ramakumar, S.

(2001) Biochem Biophys Res Commun 282: 893

  • DOI: https://doi.org/10.1006/bbrc.2001.4663
  • Primary Citation of Related Structures:  
    1HA7

  • PubMed Abstract: 

    The crystal structure of C-phycocyanin, a light-harvesting phycobiliprotein from cyanobacteria (blue-green algae) Spirulina platensis has been solved by molecular replacement technique. The crystals belong to space group P2(1) with cell parameters a = 107.20, b = 115.40, c = 183.04 A; beta = 90.2 degrees. The structure has been refined to a crystallographic R factor of 19.2% (R(free) = 23.9%) using the X-ray diffraction data extending up to 2.2 A resolution. The asymmetric unit of the crystal cell consists of two (alphabeta)6-hexamers, each hexamer being the functional unit in the native antenna rod of cyanobacteria. The molecular structure resembles that of other reported C-phycocyanins. However, the unique form of aggregation of two (alphabeta)6-hexamers in the crystal asymmetric unit, suggests additional pathways of energy transfer in lateral direction between the adjacent hexamers involving beta155 phycocyanobilin chromophores.

    • Organizational Affiliation: 

    Department of Physics, Indian Institute of Science, Bangalore, 560 012, India.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-PHYCOCYANIN ALPHA CHAIN
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
162Arthrospira platensisMutation(s): 0 
UniProt
Find proteins for P72509 (Arthrospira platensis)
Explore P72509 
Go to UniProtKB:  P72509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72509
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 CHAIN
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
172Arthrospira platensisMutation(s): 0 
UniProt
Find proteins for P72508 (Arthrospira platensis)
Explore P72508 
Go to UniProtKB:  P72508
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72508
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC
Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth T]
BA [auth C]
BB [auth T]
CA [auth D]
AA [auth B],
AB [auth T],
BA [auth C],
BB [auth T],
CA [auth D],
CB [auth U],
DA [auth D],
DB [auth V],
EA [auth E],
EB [auth V],
FA [auth F],
FB [auth W],
GA [auth F],
GB [auth X],
HA [auth G],
HB [auth X],
IA [auth H],
JA [auth H],
KA [auth I],
LA [auth J],
MA [auth J],
NA [auth K],
OA [auth L],
PA [auth L],
QA [auth M],
RA [auth N],
SA [auth N],
TA [auth O],
UA [auth P],
VA [auth P],
WA [auth Q],
XA [auth R],
Y [auth A],
YA [auth R],
Z [auth B],
ZA [auth S]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.2α = 90
b = 115.4β = 90.21
c = 183.04γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-28
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description