6GIW | pdb_00006giw

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


Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/s41477-018-0273-z
  • Primary Citation 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.


  • Organizational Affiliation
    • Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Water-soluble chlorophyll protein
A, B, C, D
180Lepidium virginicumMutation(s): 1 
Gene Names: WSCP1
UniProt
Find proteins for O04797 (Lepidium virginicum)
Explore O04797 
Go to UniProtKB:  O04797
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO04797
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.277 (Depositor) 
  • R-Value Work:  0.234 (Depositor) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 81.71β = 90
c = 121.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 2.0: 2024-01-17
    Changes: Data collection, Database references, Non-polymer description, Refinement description
  • Version 2.1: 2024-11-13
    Changes: Structure summary