2X1Z | pdb_00002x1z

Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-d

• PDB DOI: https://doi.org/10.2210/pdb2X1Z/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Amphidinium carterae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-09 Released: 2010-02-09 
• Deposition Author(s): Schulte, T., Hiller, R.G., Hofmann, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls.

Schulte, T., Hiller, R.G., Hofmann, E.

(2010) FEBS Lett 584: 973

• PubMed: 20102711 
• DOI: https://doi.org/10.1016/j.febslet.2010.01.041
• Primary Citation Related Structures: 
  2X1Z, 2X20, 2X21


• PubMed Abstract: 
  

  The peridinin-chlorophyll a-protein (PCP) from dinoflagellates is a soluble light harvesting antenna which gathers incoming photons mainly by the carotenoid peridinin. In PCPs reconstituted with different chlorophylls, the peridinin to chlorophyll energy transfer rates are well predicted by a Förster-like theory, but only if the pigment arrangements are identical in all PCPs. We have determined the X-ray structures of PCPs reconstituted with Chlorophyll-b (Chl-b), Chlorophyll-d (Chl-d) and Bacteriochlorophyll-a (BChl-a) to resolutions

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Organizational Affiliation: 
• Biophysics, Department of Biology and Biotechnology, Ruhr-University Bochum, D-44780 Bochum, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.29 kDa 
• Atom Count: 1,758 
• Modeled Residue Count: 151 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC	A [auth M]	151	Amphidinium carterae	Mutation(s): 0
UniProt
Find proteins for P80484 (Amphidinium carterae) Explore P80484  Go to UniProtKB:  P80484

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	G [auth M]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CL7	F [auth M]	CHLOROPHYLL D C54 H70 Mg N4 O6 FBCRYORFRGRJBC-ACDPFEIMSA-L
PID	B [auth M], C [auth M], D [auth M], E [auth M]	PERIDININ C39 H50 O7 UYRDHEJRPVSJFM-FROCQLDGSA-N
CD	O [auth M], P [auth M], Q [auth M], R [auth M], S [auth M], T [auth M]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG	L [auth M]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	H [auth M], I [auth M], M, N [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	J [auth M], K [auth M]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.58	α = 90
b = 81.99	β = 90
c = 75.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Schulte, T., Hiller, R.G., Hofmann, E.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description