1PPR

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae.

Hofmann, E.Wrench, P.M.Sharples, F.P.Hiller, R.G.Welte, W.Diederichs, K.

(1996) Science 272: 1788-1791

  • DOI: 10.1126/science.272.5269.1788
  • Primary Citation of Related Structures:  
    1PPR

  • PubMed Abstract: 
  • Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains ...

    Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of a Peridinin-Chlorophyll a Protein from Amphidinium Carterae
      Steck, K., Wacker, T., Welte, W., Sharples, F.P., Hiller, R.G.
      (1990) FEBS Lett 268: 48

    Organizational Affiliation

    Fakultät für Biologie, Universität Konstanz, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PERIDININ-CHLOROPHYLL PROTEINA [auth M],
B [auth N],
C [auth O]
312Amphidinium carteraeMutation(s): 0 
UniProt
Find proteins for P80484 (Amphidinium carterae)
Explore P80484 
Go to UniProtKB:  P80484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80484
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
AA [auth N],
BA [auth O],
MA [auth O],
N [auth M],
O [auth M],
AA [auth N],
BA [auth O],
MA [auth O],
N [auth M],
O [auth M],
Z [auth N]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

Download Ideal Coordinates CCD File 
CA [auth O],
D [auth M],
DA [auth O],
E [auth M],
P [auth N],
CA [auth O],
D [auth M],
DA [auth O],
E [auth M],
P [auth N],
Q [auth N]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PID
Query on PID

Download Ideal Coordinates CCD File 
EA [auth O],
F [auth M],
FA [auth O],
G [auth M],
GA [auth O],
EA [auth O],
F [auth M],
FA [auth O],
G [auth M],
GA [auth O],
H [auth M],
HA [auth O],
I [auth M],
IA [auth O],
J [auth M],
JA [auth O],
K [auth M],
KA [auth O],
L [auth M],
LA [auth O],
M,
R [auth N],
S [auth N],
T [auth N],
U [auth N],
V [auth N],
W [auth N],
X [auth N],
Y [auth N]
PERIDININ
C39 H50 O7
UYRDHEJRPVSJFM-FROCQLDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.426α = 90
b = 116.296β = 94.89
c = 67.025γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-17
    Changes: Other