1PPR

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE

• PDB DOI: https://doi.org/10.2210/pdb1PPR/pdb

• Classification: LIGHT-HARVESTING PROTEIN
• Organism(s): Amphidinium carterae
• Mutation(s): No 


• Deposited: 1996-03-06 Released: 1997-08-20 
• Deposition Author(s): Hofmann, E., Welte, W., Diederichs, K.

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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 

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

• PubMed: 8650577 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Fakultät für Biologie, Universität Konstanz, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123.8 kDa 
• Atom Count: 9,152 
• Modelled Residue Count: 936 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIDININ-CHLOROPHYLL PROTEIN	A [auth M], B [auth N], C [auth O]	312	Amphidinium carterae	Mutation(s): 0
UniProt
Find proteins for P80484 (Amphidinium carterae) Explore P80484  Go to UniProtKB:  P80484

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	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
CLA	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
PID	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

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 = 198.426	α = 90
b = 116.296	β = 94.89
c = 67.025	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-08-20 
Deposition Author(s): Hofmann, E., Welte, W., Diederichs, K.

Revision History  

• 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
• Version 2.0: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other