2YYW | pdb_00002yyw

The F20M mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F

• PDB DOI: https://doi.org/10.2210/pdb2YYW/pdb

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


• Deposited: 2007-05-02 Released: 2008-05-06 
• Deposition Author(s): Higuchi, Y., Komori, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.170 (DCC) 
• R-Value Work: 
  0.120 (DCC) 

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)

Macromolecule Content 

• Total Structure Weight: 14.01 kDa 
• Atom Count: 1,219 
• Modeled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c3	A	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
HEM	B [auth A], C [auth A], D [auth A], E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.170 (DCC) 
• R-Value Work:  0.120 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.158	α = 90
b = 67.423	β = 90
c = 34.388	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Higuchi, Y., Komori, H.

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-23
  Changes: Data collection, Structure summary