3M97

Structure of the soluble domain of cytochrome c552 with its flexible linker segment from Paracoccus denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


Literature

Structure at 1.5 A resolution of cytochrome c(552) with its flexible linker segment, a membrane-anchored protein from Paracoccus denitrificans.

Rajendran, C.Ermler, U.Ludwig, B.Michel, H.

(2010) Acta Crystallogr D Biol Crystallogr 66: 850-854

  • DOI: https://doi.org/10.1107/S0907444910019396
  • Primary Citation of Related Structures:  
    3M97

  • PubMed Abstract: 

    Electron transfer (ET) between the large membrane-integral redox complexes in the terminal part of the respiratory chain is mediated either by a soluble c-type cytochrome, as in mitochondria, or by a membrane-anchored cytochrome c, as described for the ET chain of the bacterium Paracoccus denitrificans. Here, the structure of cytochrome c(552) from P. denitrificans with the linker segment that attaches the globular domain to the membrane anchor is presented. Cytochrome c(552) including the linker segment was crystallized and its structure was determined by molecular replacement. The structural features provide functionally important information. The prediction of the flexibility of the linker region [Berry & Trumpower (1985), J. Biol. Chem. 260, 2458-2467] was confirmed by our crystal structure. The N-terminal region from residues 13 to 31 is characterized by poor electron density, which is compatible with high mobility of this region. This result indicates that this region is highly flexible, which is functionally important for this protein to shuttle electrons between complexes III and IV in the respiratory chain. Zinc present in the crystallization buffer played a key role in the successful crystallization of this protein. It provided rigidity to the long negatively charged flexible loop by coordinating negatively charged residues from two different molecules and by enhancing the crystal contacts.


  • Organizational Affiliation

    Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, Frankfurt am Main, Germany. chitra.rajendran@psi.ch


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-552A [auth X]140Paracoccus denitrificansMutation(s): 0 
Gene Names: cycM
UniProt
Find proteins for P54820 (Paracoccus denitrificans)
Explore P54820 
Go to UniProtKB:  P54820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54820
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.376α = 90
b = 38.991β = 90
c = 93.014γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description