6GIW

Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum (Mutation L91P) with Chlorophyll-a

• PDB DOI:  https://doi.org/10.2210/pdb6GIW/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lepidium virginicum
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2018-05-15 Released: 2018-10-17 
• Deposition Author(s): Palm, D.M., Agostini, A., Averesch, V., Girr, P., Werwie, M., Takahashi, S., Satoh, H., Jaenicke, E., Paulsen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Literature

Chlorophyll a/b binding-specificity in water-soluble chlorophyll protein.

Palm, D.M., Agostini, A., Averesch, V., Girr, P., Werwie, M., Takahashi, S., Satoh, H., Jaenicke, E., Paulsen, H.

(2018) Nat Plants 4: 920-929

• PubMed: 30297830 
• DOI: https://doi.org/10.1038/s41477-018-0273-z
• Primary Citation of Related Structures:  
  6GIW, 6GIX


• PubMed Abstract: 
  

We altered the chlorophyll (Chl) binding sites in various versions of water-soluble chlorophyll protein (WSCP) by amino acid exchanges to alter their preferences for either Chl a or Chl b. WSCP is ideally suited for this mutational analysis since it forms a tetrameric complex with only four identical Chl binding sites. A loop of 4-6 amino acids is responsible for Chl a versus Chl b selectivity. We show that a single amino acid exchange within this loop changes the relative Chl a/b affinities by a factor of 40. We obtained crystal structures of this WSCP variant binding either Chl a or Chl b. The Chl binding sites in these structures were compared with those in the major light-harvesting complex (LHCII) of the photosynthetic apparatus in plants to search for similar structural features involved in Chl a/b binding specificity.

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Organizational Affiliation: 

Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 81.88 kDa 
• Atom Count: 5,147 
• Modelled Residue Count: 631 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Water-soluble chlorophyll protein	A, B, C, D	180	Lepidium virginicum	Mutation(s): 1  Gene Names: WSCP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	E [auth A], F [auth B], G [auth C], H [auth D]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.72	α = 90
b = 81.71	β = 90
c = 121.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Palm, D.M., Agostini, A., Averesch, V., Girr, P., Werwie, M., Takahashi, S., Satoh, H., Jaenicke, E., Paulsen, H.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references