1C7M

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced state.

Pristovsek, P.Lucke, C.Reincke, B.Ludwig, B.Ruterjans, H.

(2000) Eur.J.Biochem. 267: 4205-4212


  • PubMed Abstract: 
  • In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Us ...

    In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Using uniformly 15N-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance NMR experiments was employed to achieve complete 1H and 15N assignments. A total of 1893 distance restraints was derived from homonuclear 2D-NOESY and heteronuclear 3D-NOESY spectra; 1486 meaningful restraints were used in the structure calculations. After restrained energy minimization a family of 20 structures was obtained with rmsd values of 0.56 +/- 0. 10 A and 1.09 +/- 0.09 A for the backbone and heavy atoms, respectively. The overall topology is similar to that seen in previously reported models of this class of proteins. The global fold consists of two long helices at the N-terminus and C-terminus and three shorter helices surrounding the heme moiety; the helices are connected by well-defined loops. Comparison with the X-ray structure shows some minor differences in the positions of the Trp57 and Phe65 side-chain rings as well as the heme propionate groups.


    Related Citations: 
    • Heterologous Expression of Soluble Fragments of Cytochrome C552 Acting as Electron Donor to the Paracoccus Denitrificans Cytochrome C Oxidase
      Reincke, B.,Thoeny-Meyer, L.,Dannehl, C.,Odenwald, A.,Aidim, M.,Witt, H.,Rueterjans, H.,Ludwig, B.
      (1999) Biochim.Biophys.Acta 1441: 114
    • Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States
      Harrenga, A.,Reincke, B.,Rueterjans, H.,Ludwig, B.,Michel, H.
      (2000) J.Mol.Biol. 295: 667


    Organizational Affiliation

    Institute of Biophysical Chemistry, J.W. Goethe-University of Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CYTOCHROME C552)
A
100Paracoccus denitrificansGene Names: cycM
Find proteins for P54820 (Paracoccus denitrificans)
Go to UniProtKB:  P54820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS 
  • Olderado: 1C7M Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance