1A7V

CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.

Shibata, N.Iba, S.Misaki, S.Meyer, T.E.Bartsch, R.G.Cusanovich, M.A.Morimoto, Y.Higuchi, Y.Yasuoka, N.

(1998) J.Mol.Biol. 284: 751-760

  • DOI: 10.1006/jmbi.1998.2190

  • PubMed Abstract: 
  • The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However th ...

    The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However the amino acid composition of the surface of helices A and B in RPCP is remarkably different from that of the dimeric cytochromes c'. This surface forms the dimer interface in the latter proteins. RPCP has seven charged residues on this surface contrary to the dimeric cytochromes c', which have only two or three charged groups on the corresponding surface. Moreover, hydrophobic residues on this surface of RPCP are two to three times fewer than in dimeric cytochromes c'. As a result of the difference in amino acid composition, the A-B surface of RPCP is rather hydrophilic compared with dimeric cytochromes c'. We thus suggest that RPCP is monomeric in solution because of the hydrophilic nature of the A-B surface. The amino acid composition of the A-B surface is similar to that of Rhodobacter capsulatus cytochrome c' (RCCP), which is an equilibrium admixture of monomer and dimer. The charge distribution of the A-B surface in RCCP, however, is considerably different from that of RPCP. Due to the difference, RCCP can form dimers by both ionic and hydrophobic interactions. These dimers are quite different from those in proteins which form strong dimers such as in Chromatium vinosum, Rhodospirillum rubrum, Rhodospirillum molischianum and Alcaligenes. Cytochrome c' can be classified into two types. Type 1 cytochromes c' have hydrophobic A-B surfaces and they are globular. The A-B surface of type 2 cytochromes c' is hydrophilic and they take a monomeric or flattened dimeric form.


    Organizational Affiliation

    Faculty of Science, Himeji Institute of Technology, Hyogo, 678-1297, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A, B
125Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 0 
Gene Names: cycA
Find proteins for P00149 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Go to UniProtKB:  P00149
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.000α = 90.00
b = 113.500β = 90.00
c = 34.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance