5DF5 | pdb_00005df5

The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.

• PDB DOI: https://doi.org/10.2210/pdb5DF5/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-26 Released: 2016-09-14 
• Deposition Author(s): Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.

Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

To be published.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.21 kDa 
• Atom Count: 3,787 
• Modeled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, somatic	A, B, C, D	104	Rattus norvegicus	Mutation(s): 0  Gene Names: Cycs
UniProt
Find proteins for P62898 (Rattus norvegicus) Explore P62898  Go to UniProtKB:  P62898

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	E [auth A], F [auth B], I [auth C], K [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
FC6	G [auth B], H [auth B], J [auth C]	HEXACYANOFERRATE(3-) C6 Fe N6 HCMVSLMENOCDCK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.609	α = 110.01
b = 51.739	β = 93.09
c = 61.748	γ = 91.88

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	NIGMS RO1 089900

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary