2Z47

The Y66L mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F

• PDB DOI: https://doi.org/10.2210/pdb2Z47/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
• Expression System: Shewanella
• Mutation(s): Yes 


• Deposited: 2007-06-13 Released: 2008-06-17 
• Deposition Author(s): Higuchi, Y., Komori, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structures of Noncoordinated Aromatic Residue Mutants in Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Takayama, Y., Komori, H., Morita, K., Higuchi, Y., Akutsu, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.96 kDa 
• Atom Count: 2,169 
• Modelled Residue Count: 214 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c3	A, B	107	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 1
UniProt
Find proteins for P00132 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P00132  Go to UniProtKB:  P00132

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.424	α = 90
b = 69.558	β = 92.73
c = 53.749	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Higuchi, Y., Komori, H.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-10-02
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Derived calculations
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-20
  Changes: Structure summary