1DUW

STRUCTURE OF NONAHEME CYTOCHROME C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution.

Umhau, S.Fritz, G.Diederichs, K.Breed, J.Welte, W.Kroneck, P.M.

(2001) Biochemistry 40: 1308-1316


  • PubMed Abstract: 
  • A nine heme group containing cytochrome c isolated from the soluble and membrane fractions of Desulfovibrio desulfuricans Essex, termed nonaheme cytochrome c, was crystallized, and the structure was solved using the multiple wavelength anomalous disp ...

    A nine heme group containing cytochrome c isolated from the soluble and membrane fractions of Desulfovibrio desulfuricans Essex, termed nonaheme cytochrome c, was crystallized, and the structure was solved using the multiple wavelength anomalous dispersion (MAD) phasing method. Refinement was carried out to a resolution of 1.89 A, and anisotropic temperature factors were addressed to the iron and sulfur atoms in the model. The structure revealed two cytochrome c(3) like domains with the typical arrangement of four heme centers. Both domains flanked an extra heme buried under the protein surface. This heme is held in position by loop extensions in each of the two domains. Although both the N- and C-terminal tetraheme domains exhibit a fold and heme arrangement very similar to that of cytochrome c(3), they differ considerably in their loop extensions and electrostatic surface. Analysis of the structure provides evidence for a different function of both domains, namely, anchoring the protein in a transmembranous complex with the N-terminal domain and formation of an electron-transfer complex with hydrogenase by the C-terminal domain.


    Organizational Affiliation

    Fachbereich Biologie, Mathematisch-Naturwissenschaftliche Sektion, Universit├Ąt Konstanz, 78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NONAHEME CYTOCHROME C
A
292Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: hmcA
Find proteins for Q9XCU0 (Desulfovibrio desulfuricans)
Go to UniProtKB:  Q9XCU0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 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: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.400α = 90.00
b = 55.400β = 90.00
c = 236.800γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
XDSdata scaling
SHELXL-97refinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation