1NBB

N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus.

Tahirov, T.H.Misaki, S.Meyer, T.E.Cusanovich, M.A.Higuchi, Y.Yasuoka, N.

(1996) Nat.Struct.Mol.Biol. 3: 459-464


  • PubMed Abstract: 
  • We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are signif ...

    We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are significant conformational changes of amino acid residues in the haem vicinity, accompanied by a rearrangement of the hydrogen bonding pattern. The results suggest that rearrangements resulting from ligand binding could drive dimer dissociation in some species and also that the haem propionate may participate in proton transfer.


    Related Citations: 
    • High-Resolution Crystal Structures of Two Polymorphs of Cytochrome C' from the Purple Phototrophic Bacterium Rhodobacter Capsulatus
      Tahirov, T.H.,Misaki, S.,Meyer, T.E.,Cusanovich, M.A.,Higuchi, Y.,Yasuoka, N.
      (1996) J.Mol.Biol. 259: 467
    • Crystal Structures of Cytochrome C' from Rhodobacter Capsulatus Strain St. Louis
      Tahirov, T.H.,Misaki, S.,Meyer, T.E.,Cusanovich, M.A.,Yasuoka, N.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A, B
129Rhodobacter capsulatusN/A
Find proteins for P00147 (Rhodobacter capsulatus)
Go to UniProtKB:  P00147
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NBN
Query on NBN

Download SDF File 
Download CCD File 
A, B
N-BUTYL ISOCYANIDE
C5 H9 N
FSBLVBBRXSCOKU-UHFFFAOYSA-N
 Ligand Interaction
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: 2.4 Å
  • R-Value Work: 0.174 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.734α = 90.00
b = 70.535β = 87.02
c = 89.652γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance