6HRN

C-Phycocyanin from heterocyst forming filamentous cyanobacterium Nostoc sp. WR13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of phycocyanin from heterocyst-forming filamentous cyanobacterium Nostoc sp. WR13.

Patel, H.M.Roszak, A.W.Madamwar, D.Cogdell, R.J.

(2019) Int J Biol Macromol 135: 62-68

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.05.099
  • Primary Citation of Related Structures:  
    6HRN

  • PubMed Abstract: 

    Phycocyanin (PC) is the principal pigment protein in the light-harvesting antenna of cyanobacteria. Here the biochemical characterization and the 1.51 Å crystal structure of PC from cyanobacterium Nostoc sp. WR13 (Nst-PC) is reported. The P6 3 crystal lattice is composed of the minimal biological entities of Nst-PC, the (αβ) 3 trimeric rings. The structure has been refined to R factor 11.5% (R free 15.4%) using anisotropic atomic B factors. A phylogenetic study shows that the α and β chains of Nst-PC are significantly clustered in a distinct clade with Acaryochloris marina. The structure was examined to look for any significant differences between Nst-PC and PC from non-desert species. Only minor differences were found in the chromophore microenvironments. The tentative energy transfer pathways in Nst-PC were modeled based on simple structural considerations.


  • Organizational Affiliation

    P. G. Department of Biosciences, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, 388315 Anand, Gujarat, India; Institute of Molecular Cell and Systems Biology, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK. Electronic address: hiralpatel2387@yahoo.co.in.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha Subunit of Cyanobacterial Phycocyanin protein162Nostoc sp.Mutation(s): 0 
UniProt
Find proteins for A0A509GUZ8 (Nostoc sp)
Explore A0A509GUZ8 
Go to UniProtKB:  A0A509GUZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A509GUZ8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta Subunit of Cyanobacterial Phycocyanin protein172Nostoc sp.Mutation(s): 0 
UniProt
Find proteins for A0A509GUZ9 (Nostoc sp)
Explore A0A509GUZ9 
Go to UniProtKB:  A0A509GUZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A509GUZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B],
G [auth B]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
Q [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

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H [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO3
Query on NO3

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P [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.473α = 90
b = 151.473β = 90
c = 39.764γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
AutoPROCdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references