1GH0

CRYSTAL STRUCTURE OF C-PHYCOCYANIN FROM SPIRULINA PLATENSIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Structure of C-phycocyanin from Spirulina platensis at 2.2 A resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes.

Wang, X.Q., Li, L.N., Chang, W.R., Zhang, J.P., Gui, L.L., Guo, B.J., Liang, D.C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 784-792

  • DOI: 10.1107/s0907444901004528
  • Primary Citation of Related Structures:  
    1GH0

  • PubMed Abstract: 

    • The crystal structure of C-phycocyanin from the cyanobacterium S. platensis has been determined at 2.2 A resolution. The crystals belong to the monoclinic crystal form, which has not been previously reported for phycobiliprotein structures. The structure was solved using the molecular-replacement method with a final R value of 18 ...

    The crystal structure of C-phycocyanin from the cyanobacterium S. platensis has been determined at 2.2 A resolution. The crystals belong to the monoclinic crystal form, which has not been previously reported for phycobiliprotein structures. The structure was solved using the molecular-replacement method with a final R value of 18.9% (R(free) = 23.7%) after model building and refinement. In the crystals used for the study, the C-phycocyanin hexamers formed by face-to-face association of two trimers are arranged in layers rather than in columns. Three different kinds of packing between adjacent hexamers in the layer were compared. The tight packing of two adjacent hexamers formed by four trimers in the asymmetric unit brings beta155 PCB chromophores close together, so it is possible that lateral energy transfer takes place through the beta155-beta155 route.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-PHYCOCYANIN ALPHA SUBUNIT
A, C, E, G, I, K, M, O, Q, S, U, W
A, C, E, G, I, K, M, O, Q, S, U, W
162Arthrospira platensisMutation(s): 0 
Gene Names: cpcA
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-PHYCOCYANIN BETA SUBUNIT
B, D, F, H, J, L, N, P, R, T, V, X
B, D, F, H, J, L, N, P, R, T, V, X
172Arthrospira platensisMutation(s): 1 
Gene Names: cpcB
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H, J, L, N, P, R, T, V, X
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: 0.237 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109α = 90
b = 117.5β = 90.3
c = 185γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection