6K9I | pdb_00006k9i

High-resolution three-dimensional structure of horse heart cytochrome C at room temperature

• PDB DOI: https://doi.org/10.2210/pdb6K9I/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): Yes 


• Deposited: 2019-06-16 Released: 2020-06-17 
• Deposition Author(s): Sugawara, Y., Endo, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

High-resolution three-dimensional structure of horse heart cytochrome C

Fujita, T., Yamamura, S., Endo, S., Sugawara, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.37 kDa 
• Atom Count: 909 
• Modeled Residue Count: 105 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A	105	Equus caballus	Mutation(s): 1
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004  Go to UniProtKB:  P00004

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.395	α = 90
b = 58.395	β = 90
c = 41.909	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Sugawara, Y., Endo, S.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary