1C53

S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.

Nakagawa, A.Higuchi, Y.Yasuoka, N.Katsube, Y.Yagi, T.

(1990) J.Biochem.(Tokyo) 108: 701-703


  • PubMed Abstract: 
  • The three-dimensional structure of cytochrome c-553 isolated from sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F strain, has been determined by the multi-wavelength anomalous dispersion technique with use of synchrotron radiation. The ...

    The three-dimensional structure of cytochrome c-553 isolated from sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F strain, has been determined by the multi-wavelength anomalous dispersion technique with use of synchrotron radiation. The result shows that bacterial S-class cytochromes c have a variety of folding patterns. The relative location of two a-helices at amino- and carboxyl-terminals and the style of bonding to the heme group show "cytochrome c folding," but other regions of the structure are different from those of other cytochromes c previously reported. The results also give useful information about the location of sulfate-reducing bacterium on the phylogenetic tree of the bacterial cytochromes c superfamily.


    Related Citations: 
    • Structure Determination of Cytochrome C-553 from Desulfovibrio Vulgaris Miyazaki F Determined by the Multi-Wavelength Anomalous Dispersion Method
      Nakagawa, A.,Higuchi, Y.,Yasuoka, N.,Katsube, Y.,Yagi, T.
      (1990) Acta Crystallogr.,Sect.A 46: 16
    • Crystallographic Study of Cytochrome C553 from Desulfovibrio Vulgaris Miyazaki
      Nakagawa, A.,Nagashima, E.,Higuchi, Y.,Kusunoki, M.,Matsuura, Y.,Yasuoka, N.,Katsube, Y.,Chihara, H.,Yagi, T.
      (1986) J.Biochem.(Tokyo) 99: 605


    Organizational Affiliation

    Photon Factory, National Laboratory for High Energy Physics, Hyogo.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C553
A
79Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)N/A
Find proteins for P00120 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P00120
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.8 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.700α = 90.00
b = 42.700β = 90.00
c = 103.400γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance