Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Structural Characterization of Nitrosomonas Europaea Cytochrome C-552 Variants with Marked Differences in Electronic Structure.

Can, M.Krucinska, J.Zoppellaro, G.Andersen, N.H.Wedekind, J.E.Hersleth, H.-P.Andersson, K.K.Bren, K.L.

(2013) Chembiochem 14: 1828

  • DOI: https://doi.org/10.1002/cbic.201300118
  • Primary Citation of Related Structures:  
    3ZOW, 3ZOX, 3ZOY, 4JCG

  • PubMed Abstract: 

    Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.

  • Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, NY 14627 (USA).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
81Nitrosomonas europaeaMutation(s): 0 
Find proteins for P95339 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore P95339 
Go to UniProtKB:  P95339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95339
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
EA [auth M]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
HA [auth P],
IA [auth Q],
JA [auth R],
S [auth A],
T [auth B],
U [auth C],
V [auth D],
W [auth E],
X [auth F],
Y [auth G],
Z [auth H]
C34 H34 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.45α = 90
b = 137.93β = 90
c = 204.66γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description