5YHJ | pdb_00005yhj

Cytochrome P450EX alpha (CYP152N1) wild-type with myristic acid

• PDB DOI: https://doi.org/10.2210/pdb5YHJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Exiguobacterium sp. AT1b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-28 Released: 2017-12-06 
• Deposition Author(s): Onoda, H., Shoji, O., Suzuki, K., Sugimoto, H., Shiro, Y., Watanabe, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), The Ministry of Education,Culture,Sports,Science and Technology(MEXT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Alpha-Oxidative Decarboxylation of Fatty Acids Catalysed by Cytochrome P450 Peroxygenases Yielding Shorter-Alkyl-Chain Fatty Acids

Onoda, H., Shoji, O., Suzuki, K., Sugimoto, H., Shiro, Y., Watanabe, Y.

(2017) Catal Sci Technol 

• DOI: https://doi.org/10.1039/C7CY02263H

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.02 kDa 
• Atom Count: 6,834 
• Modeled Residue Count: 817 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B	413	Exiguobacterium sp. AT1b	Mutation(s): 0  Gene Names: EAT1b_2299
UniProt
Find proteins for C4L2G9 (Exiguobacterium sp. (strain ATCC BAA-1283 / AT1b)) Explore C4L2G9  Go to UniProtKB:  C4L2G9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MYR	D [auth A], F [auth B]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.962	α = 90
b = 58.962	β = 90
c = 238.348	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Onoda, H., Shoji, O., Suzuki, K., Sugimoto, H., Shiro, Y., Watanabe, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16J02846
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)	Japan	15H05806
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)	Japan	17H03087

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations