6C4W | pdb_00006c4w

Structure of the yeast Pichia membranifaciens cytochrome c

• PDB DOI: https://doi.org/10.2210/pdb6C4W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pichia membranifaciens
• Mutation(s): No 


• Deposited: 2018-01-13 Released: 2018-02-07 
• Deposition Author(s): McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.330 (Depositor), 0.337 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Characterization of two crystal forms of cytochrome c from Valida membranifaciens

Day, J., McPherson, A.

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: 12.8 kDa 
• Atom Count: 970 
• Modeled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c	A	109	Pichia membranifaciens	Mutation(s): 0
UniProt
Find proteins for A0A3B6UES8 (Pichia membranifaciens) Explore A0A3B6UES8  Go to UniProtKB:  A0A3B6UES8

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	A	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.330 (Depositor), 0.337 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.968	α = 90
b = 63.715	β = 90
c = 64.322	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): McPherson, A.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary