5HPZ | pdb_00005hpz

type II water soluble Chl binding proteins

• PDB DOI: https://doi.org/10.2210/pdb5HPZ/pdb

• Classification: Chlorophyll binding protein
• Organism(s): Brassicaceae
• Expression System: Atlantibacter hermannii
• Mutation(s): No 


• Deposited: 2016-01-21 Released: 2016-05-04 
• Deposition Author(s): Bednarczyk, D., Dym, O., Prabahard, V., Noy, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Fine Tuning of Chlorophyll Spectra by Protein-Induced Ring Deformation.

Bednarczyk, D., Dym, O., Prabahar, V., Peleg, Y., Pike, D.H., Noy, D.

(2016) Angew Chem Int Ed Engl 55: 6901-6905

• PubMed: 27098554 
• DOI: https://doi.org/10.1002/anie.201512001
• Primary Citation Related Structures: 
  5HPZ


• PubMed Abstract: 
  

  The ability to tune the light-absorption properties of chlorophylls by their protein environment is the key to the robustness and high efficiency of photosynthetic light-harvesting proteins. Unfortunately, the intricacy of the natural complexes makes it very difficult to identify and isolate specific protein-pigment interactions that underlie the spectral-tuning mechanisms. Herein we identify and demonstrate the tuning mechanism of chlorophyll spectra in type II water-soluble chlorophyll binding proteins from Brassicaceae (WSCPs). By comparing the molecular structures of two natural WSCPs we correlate a shift in the chlorophyll red absorption band with deformation of its tetrapyrrole macrocycle that is induced by changing the position of a nearby tryptophan residue. We show by a set of reciprocal point mutations that this change accounts for up to 2/3 of the observed spectral shift between the two natural variants.

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Organizational Affiliation: 
• Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel.
Migal-Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel.
Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
Migal-Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.11 kDa 
• Atom Count: 2,727 
• Modeled Residue Count: 350 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Water-soluble chlorophyll protein	A, B	179	Brassicaceae	Mutation(s): 0  Gene Names: WSCP1R
UniProt
Find proteins for Q8H0F0 (Brassica oleracea var. viridis) Explore Q8H0F0  Go to UniProtKB:  Q8H0F0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
68G	C [auth A], D [auth B]	13'2-hydroxyl-Chlorophyll a C55 H72 Mg N4 O6 OEXIMXLSKZYECT-SUXMITRLSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.92	α = 90
b = 95.479	β = 90
c = 98.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Bednarczyk, D., Dym, O., Prabahard, V., Noy, D.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-05-18
  Changes: Derived calculations
• Version 1.2: 2016-06-08
  Changes: Database references
• Version 1.3: 2019-05-29
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary