4K7B

Crystal structure of Extrinsic protein in photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Psb31, a Novel Extrinsic Protein of Photosystem II from a Marine Centric Diatom and Implications for Its Binding and Function

Nagao, R.Suga, M.Niikura, A.Okumura, A.Koua, F.H.Suzuki, T.Tomo, T.Enami, I.Shen, J.R.

(2013) Biochemistry 52: 6646-6652

  • DOI: 10.1021/bi400770d

  • PubMed Abstract: 
  • Psb31 is a fifth extrinsic protein found in photosystem II (PSII) of a centric diatom, Chaetoceros gracilis . The protein has been shown to bind directly to PSII in the absence of other extrinsic proteins and serves in part as a substitute for PsbO i ...

    Psb31 is a fifth extrinsic protein found in photosystem II (PSII) of a centric diatom, Chaetoceros gracilis . The protein has been shown to bind directly to PSII in the absence of other extrinsic proteins and serves in part as a substitute for PsbO in supporting oxygen evolution. We report here the crystal structure of Psb31 at a resolution of 1.55 Å. The structure of Psb31 was composed of two domains, one major, N-terminal four helical domain and one minor, flexible C-terminal domain. The four helices in the N-terminal domain were arranged in an up-down-up-down fold, which appeared unexpectedly to be similar to the structure of spinach PsbQ, in spite of their low sequence homology. This suggests that the centric diatom PSII contains another PsbQ-type extrinsic protein in addition to the original PsbQ protein found in the organism. On the other hand, the C-terminal domain of Psb31 has a unique structure composed of one loop and one short helix. Based on these structural analysis and chemical cross-linking experiments, residues responsible for the binding of Psb31 to PSII intrinsic proteins were suggested. The results are discussed in relation to the copy number of extrinsic proteins in higher plant PSII.


    Organizational Affiliation

    Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University , Sakurajosui 3-25-40, Setagaya-ku, Tokyo 156-8850, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem II
A
124Chaetoceros gracilisGene Names: psb31
Find proteins for B6ZHE7 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHE7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.411α = 90.00
b = 92.411β = 90.00
c = 31.283γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXDphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SHELXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references