6S2Y

Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum with Chlorophyll-b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein.

Agostini, A.Meneghin, E.Gewehr, L.Pedron, D.Palm, D.M.Carbonera, D.Paulsen, H.Jaenicke, E.Collini, E.

(2019) Sci Rep 9: 18255-18255

  • DOI: https://doi.org/10.1038/s41598-019-54520-4
  • Primary Citation of Related Structures:  
    6S2Y, 6S2Z

  • PubMed Abstract: 

    The Water-Soluble Chlorophyll Protein (WSCP) of Brassicaceae is a remarkably stable tetrapyrrole-binding protein that, by virtue of its simple design, is an exceptional model to investigate the interactions taking place between pigments and their protein scaffold and how they affect the photophysical properties and the functionality of the complexes. We investigated variants of WSCP from Lepidium virginicum (Lv) and Brassica oleracea (Bo), reconstituted with Chlorophyll (Chl) b, to determine the mechanisms by which the different Chl binding sites control their Chl a/b specificities. A combined Raman and crystallographic investigation has been employed, aimed to characterize in detail the hydrogen-bond network involving the formyl group of Chl b. The study revealed a variable degree of conformational freedom of the hydrogen bond networks among the WSCP variants, and an unexpected mixed presence of hydrogen-bonded and not hydrogen-bonded Chls b in the case of the L91P mutant of Lv WSCP. These findings helped to refine the description of the mechanisms underlying the different Chl a/b specificities of WSCP versions, highlighting the importance of the structural rigidity of the Chl binding site in the vicinity of the Chl b formyl group in granting a strong selectivity to binding sites.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy. alessandro.agostini.1@unipd.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Water-soluble chlorophyll protein
A, B, C, D
180Lepidium virginicumMutation(s): 0 
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: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.31α = 90
b = 82.9β = 90
c = 122.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyPa 324/10-1
Italian Ministry of EducationItalyPRIN 2015 no. 2015XBZ5YA

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description