3U99

The experimental X-ray structure of the new diheme cytochrome type c from Shewanella baltica OS155 sb-DHC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.146 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystal structure of the recombinant diheme cytochrome c from Shewanella baltica (OS155).

De March, M.Di Rocco, G.Hickey, N.Geremia, S.

(2015) J.Biomol.Struct.Dyn. 33: 395-403

  • DOI: 10.1080/07391102.2014.880657

  • PubMed Abstract: 
  • Multiheme cytochromes c (cyts c) are c-type cyts characterized by non-standard structural and spectroscopic properties. The relative disposition of the heme cofactors in the core of these proteins is conserved and they can be classified from their ge ...

    Multiheme cytochromes c (cyts c) are c-type cyts characterized by non-standard structural and spectroscopic properties. The relative disposition of the heme cofactors in the core of these proteins is conserved and they can be classified from their geometry in two main groups. In one group the porphyrin planes are arranged in a perpendicular fashion, while in the other they are parallel. Orientation of the heme groups is a key factor that regulates the intramolecular electron transfer pathway. A 16.5 kDa diheme cyt c, isolated from the bacterium Shewanella baltica OS155 (Sb-DHC), was cloned and expressed in E. coli and its structure was investigated by X-ray crystallography. Using high-resolution data (1.14 Å) collected at ELETTRA (Trieste), the crystal structure, with an orthorhombic cell (a = 40.81, b = 42.97, c = 82.07 Å), was solved using the homologous diheme from Rhodobacter sphaeroides (Rs-DHC) as the initial model. The electron density map of the refined structure (Rfact of 13.8% and Rfree of 15.4%) shows a two domain structure connected by a central unstructured region (N72-G87). The Sb-DHC, like its homologue (Rs-DHC), folds into a new cyt c class: the N-terminal globular domain, with its three α-helices, belongs to class I of c-type cyts, while the C-terminal domain includes a rare π-helix. The metal centre of the c-type heme groups is axially coordinated by two His residues and it is covalently bound to the protein through two Cys bonds.


    Related Citations: 
    • Cloning, expression, and physicochemical characterization of a new diheme cytochrome c from Shewanella baltica OS155.
      Di Rocco, G.,Battistuzzi, G.,Bortolotti, C.A.,Borsari, M.,Ferrari, E.,Monari, S.,Sola, M.
      (2011) J.Biol.Inorg.Chem. 16: 461
    • Structural and functional studies on DHC, the diheme cytochrome c from Rhodobacter sphaeroides, and its interaction with SHP, the sphaeroides heme protein.
      Gibson, H.R.,Mowat, C.G.,Miles, C.S.,Li, B.R.,Leys, D.,Reid, G.A.,Chapman, S.K.
      (2006) Biochemistry 45: 6363
    • Structural and biochemical characterization of DHC2, a novel diheme cytochrome c from Geobacter sulfurreducens.
      Heitmann, D.,Einsle, O.
      (2005) Biochemistry 44: 12411
    • The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
      Brige, A.,Leys, D.,Meyer, T.E.,Cusanovich, M.A.,Van Beeumen, J.J.
      (2002) Biochemistry 41: 4827


    Organizational Affiliation

    a Centre of Excellence in Biocrystallography (CEB), Department of Chemical and Pharmaceutical Sciences , University of Trieste , via L.Giorgieri 1, 34127 Trieste , Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diheme cytochrome c
A
148Shewanella baltica (strain OS155 / ATCC BAA-1091)Mutation(s): 0 
Find proteins for A3CZ62 (Shewanella baltica (strain OS155 / ATCC BAA-1091))
Go to UniProtKB:  A3CZ62
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: X-RAY DIFFRACTION
  • Resolution: 1.146 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.810α = 90.00
b = 42.970β = 90.00
c = 81.070γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
HKL-2000data collection
MOSFLMdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Database references
  • Version 1.2: 2014-12-10
    Type: Database references