1FT5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  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 ...

    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.Mol.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C554
A
211Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298)Gene Names: cycA1, cycA2, cycA3 (cycA, hcy, cycA, cycA)
Find proteins for Q57142 (Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298))
Go to UniProtKB:  Q57142
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 147.892α = 90.00
b = 147.892β = 90.00
c = 33.913γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
X-PLORrefinement
SCALEPACKdata scaling
SHELXrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance