1BBH

ATOMIC STRUCTURE OF A CYTOCHROME C' WITH AN UNUSUAL LIGAND-CONTROLLED DIMER DISSOCIATION AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution.

Ren, Z.Meyer, T.McRee, D.E.

(1993) J.Mol.Biol. 234: 433-445

  • DOI: 10.1006/jmbi.1993.1597

  • PubMed Abstract: 
  • The crystallographic structure of cytochrome c' from the purple phototrophic bacterium Chromatium vinosum (CVCP) has been determined at 1.8 A resolution using multiple isomorphous replacement. The molecule is a dimer, with each 131-residue chain fold ...

    The crystallographic structure of cytochrome c' from the purple phototrophic bacterium Chromatium vinosum (CVCP) has been determined at 1.8 A resolution using multiple isomorphous replacement. The molecule is a dimer, with each 131-residue chain folding as a four-helical bundle incorporating a covalently bound heme group at the core. This structure is the third of the ubiquitous cytochromes c' to be solved and is similar to the known structures of cytochrome c' from R. molischianum (RMCP) and R. rubrum (RRCP). CVCP is unique in exhibiting ligand-controlled dimer dissociation while RMCP and RRCP do not. The Tyr16 side-chain, which replaced Met16 in RMCP and Leu14 in RRCP, is parallel to the heme plane and located directly above the sixth ligand site of the heme Fe. Any ligand binding to this site, such as CO or CN-, must move the Tyr16 side-chain, which would be expected to cause other conformational changes of helix A, which contributes to the dimer interface, and consequently disrupting the dimer. Thus, the crystallographic structure of CVCP suggests a mechanism for dimer dissociation upon ligand binding. The dimer interface specificity is due to a lock and key shape complementarity of hydrophobic residues and not to any charge complementarity or cross-interface hydrogen bonds as is common in other protein-protein interfaces. The co-ordinates have been deposited in the Brookhaven Data Bank (entry P1BBH).


    Related Citations: 
    • Crystallization and Characterization of Chromatium Vinosum Cytochrome C'
      Mcree, D.E.,Redford, S.M.,Meyer, T.E.,Cusanovich, M.A.
      (1990) J.Mol.Biol. 265: 5364


    Organizational Affiliation

    Department of Biochemistry, University of Arizona, Tucson 85721.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A, B
131Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)Gene Names: cycA
Find proteins for P00154 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D))
Go to UniProtKB:  P00154
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: 1.8 Å
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.200α = 90.00
b = 56.700β = 90.00
c = 98.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-05-18 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Ren, Z., Mcree, D.E.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other