1NBB | pdb_00001nbb

N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'

• PDB DOI: https://doi.org/10.2210/pdb1NBB/pdb

• Classification: ELECTRON TRANSPORT (HEME PROTEIN)
• Organism(s): Rhodobacter capsulatus
• Mutation(s): No 


• Deposited: 1996-03-18 Released: 1996-08-17 
• Deposition Author(s): Tahirov, T.H., Misaki, S., Meyer, T.E., Cusanovich, M.A., Higuchi, Y., Yasuoka, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

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 Biol 3: 459-464

• PubMed: 8612077 
• DOI: https://doi.org/10.1038/nsb0596-459
• Primary Citation Related Structures: 
  1NBB


• 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 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.

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Organizational Affiliation: 
• Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.71 kDa 
• Atom Count: 2,044 
• Modeled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C'	A, B	129	Rhodobacter capsulatus	Mutation(s): 0
UniProt
Find proteins for P00147 (Rhodobacter capsulatus) Explore P00147  Go to UniProtKB:  P00147

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NBN	D [auth A], F [auth B]	N-BUTYL ISOCYANIDE C5 H9 N FSBLVBBRXSCOKU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.734	α = 90
b = 70.535	β = 87.02
c = 89.652	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-08-17 
Deposition Author(s): Tahirov, T.H., Misaki, S., Meyer, T.E., Cusanovich, M.A., Higuchi, Y., Yasuoka, N.

Revision History  

• Version 1.0: 1996-08-17
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-11-20
  Changes: Structure summary