1FT5

CRYSTAL STRUCTURE OF THE OXIDIZED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

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This is version 1.4 of the entry. See complete history


Literature

High-resolution structures of the oxidized and reduced states of cytochrome c554 from Nitrosomonas europaea.

Iverson, T.M.Arciero, D.M.Hooper, A.B.Rees, D.C.

(2001) J Biol Inorg Chem 6: 390-397

  • DOI: 10.1007/s007750100213
  • Primary Citation of Related Structures:  
    1FT5, 1FT6

  • PubMed Abstract: 
  • Cytochrome c554 (cyt c554) is a tetra-heme cytochrome involved in the oxidation of NH3 by Nitrosomonas europaea. The X-ray crystal structures of both the oxidized and dithionite-reduced states of cyt c554 in a new, rhombohedral crystal form have been solved by molecular replacement, at 1 ...

    Cytochrome c554 (cyt c554) is a tetra-heme cytochrome involved in the oxidation of NH3 by Nitrosomonas europaea. The X-ray crystal structures of both the oxidized and dithionite-reduced states of cyt c554 in a new, rhombohedral crystal form have been solved by molecular replacement, at 1.6 A and 1.8 A resolution, respectively. Upon reduction, the conformation of the polypeptide chain changes between residues 175 and 179, which are adjacent to hemes III and IV. Cyt c554 displays conserved heme-packing motifs that are present in other heme-containing proteins. Comparisons to hydroxylamine oxidoreductase, the electron donor to cyt c554, and cytochrome c nitrite reductase, an enzyme involved in nitrite ammonification, reveal substantial structural similarity in the polypeptide chain surrounding the heme core environment. The structural determinants of these heme-packing motifs extend to the buried water molecules that hydrogen bond to the histidine ligands to the heme iron. In the original structure determination of a tetragonal crystal form, a cis peptide bond between His129 and Phe130 was identified that appeared to be stabilized by crystal contacts. In the rhombohedral crystal form used in the present high-resolution structure determination, this peptide bond adopts the trans conformation, but with disallowed angles of phi and psi.


    Related Citations: 
    • Heme Packing Motifs Revealed by the Crystal Structure of the Tetra-heme Cytochrome c554 from Nitrosomonas europaea
      Iverson, T.M., Arciero, D.M., Hsu, B.T., Logan, M.S., Hooper, A.B., Rees, D.C.
      (1998) Nat Struct Biol 5: 1005

    Organizational Affiliation

    Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, MC 147-75 CH, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C554A211Nitrosomonas europaeaMutation(s): 0 
UniProt
Find proteins for Q57142 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q57142 
Go to UniProtKB:  Q57142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57142
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.892α = 90
b = 147.892β = 90
c = 33.913γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
REFMACrefinement
AMoREphasing
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection