3AZC | pdb_00003azc

Crystal structure of the soluble part of cytochrome b6f complex iron-sulfur subunit from Thermosynechococcus elongatus BP-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.236 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structure of a thermophilic cyanobacterial b(6)f-type Rieske protein

Veit, S., Takeda, K., Tsunoyama, Y., Rexroth, D., Rogner, M., Miki, K.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1400-1408

  • DOI: https://doi.org/10.1107/S0907444912034129
  • Primary Citation of Related Structures:  
    3AZC

  • PubMed Abstract: 

    The `Rieske protein' PetC is one of the key subunits of the cytochrome b(6)f complex. Its Rieske-type [2Fe-2S] cluster participates in the photosynthetic electron-transport chain. Overexpression and careful structure analysis at 2.0 Å resolution of the extrinsic soluble domain of PetC from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled in-depth spectroscopic and structural characterization and suggested novel structural features. In particular, both the protein structure and the positions of the internal water molecules unexpectedly showed a higher similarity to eukaryotic PetCs than to other prokaryotic PetCs. The structure also revealed a deep pocket on the PetC surface which is oriented towards the membrane surface in the whole complex. Its surface properties suggest a binding site for a hydrophobic compound and the complete conservation of the pocket-forming residues in all known PetC sequences indicates the functional importance of this pocket in the cytochrome b(6)f complex.

    • Organizational Affiliation: 

    Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit133Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: petC, tlr0959
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
UniProt
Find proteins for P0C8N8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0C8N8 
Go to UniProtKB:  P0C8N8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C8N8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES
Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.324α = 90
b = 91.324β = 90
c = 43.342γ = 120
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary