PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10

Experimental Data Snapshot

  • Resolution: 1.22 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystallographic and Computational Analysis of the Barrel Part of the Psbo Protein of Photosystem II -Carboxylate-Water Clusters as Putative Proton Transfer Relays and Structural Switches

Bommer, M.Bondar, A.N.Zouni, A.Dobbek, H.Dau, H.

(2016) Biochemistry 55: 4626

  • DOI: https://doi.org/10.1021/acs.biochem.6b00441
  • Primary Citation of Related Structures:  
    5G38, 5G39, 5G3A

  • PubMed Abstract: 

    In all organisms that employ oxygenic photosynthesis, the membrane-extrinsic PsbO protein is a functionally important component of photosystem II. To study the previously proposed proton antenna function of carboxylate clusters at the protein-water interface, we combined crystallography and simulations of a truncated cyanobacterial (Thermosynechococcus elongatus) PsbO without peripheral loops. We expressed the PsbO β-barrel heterologously and determined crystal structures at resolutions of 1.15-1.5 Å at 100 K at various pH values and at 297 K and pH 6. (1) Approximately half of the 177 surface waters identified at 100 K are resolved at 297 K, suggesting significant occupancy of specific water sites at room temperature, and loss of resolvable occupancy for other sites. (2) Within a loop region specific to cyanobacterial PsbO, three residues and four waters coordinating a calcium ion are well ordered even at 297 K; the ligation differs for manganese. (3) The crystal structures show water-carboxylate clusters that could facilitate fast Grotthus-type proton transfer along the protein surface and/or store protons. (4) Two carboxylate side chains, which are part of a structural motif interrupting two β-strands and connecting PsbO to photosystem II, are within hydrogen bonding distance at pH 6 (100 K). Simulations indicate coupling between protein structure and carboxylate protonation. The crystal structure determined at 100 K and pH 10 indicates broken hydrogen bonding between the carboxylates and local structural change. At pH 6 and 297 K, both conformations were present in the crystal, suggesting conformational dynamics in the functionally relevant pH regime. Taken together, crystallography and molecular dynamics underline a possible mechanism for pH-dependent structural switching.

  • Organizational Affiliation

    Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin , Unter den Linden 6, 10099 Berlin, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE172Thermosynechococcus vestitus BP-1Mutation(s): 0 
Find proteins for P0A432 (Synechococcus elongatus)
Explore P0A432 
Go to UniProtKB:  P0A432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A432
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.22 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.695α = 90
b = 54.695β = 90
c = 192.405γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2019-03-06
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description