4WGZ | pdb_00004wgz

Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 6.0

• PDB DOI: https://doi.org/10.2210/pdb4WGZ/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Achromobacter xylosoxidans
• Mutation(s): No 


• Deposited: 2014-09-19 Released: 2015-03-18 
• Deposition Author(s): Takashina, A., Unno, M., Kohzuma, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 
  0.162 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystallographic Elucidation for the Alkaline High-spin State Transition of Iron(III) Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015

Takashina, A., Unno, M., Kohzuma, T.

(2015) Chem Lett 44: 268-270

• DOI: https://doi.org/10.1246/cl.140975

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 14.25 kDa 
• Atom Count: 1,367 
• Modeled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c'	A	127	Achromobacter xylosoxidans	Mutation(s): 0
UniProt
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans) Explore P00138  Go to UniProtKB:  P00138

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
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.162 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.189	α = 90
b = 53.189	β = 90
c = 181.026	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Takashina, A., Unno, M., Kohzuma, T.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 2.0: 2020-01-29
  Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary