3VNO

Cytochrome P450SP alpha (CYP152B1) mutant R241E

• PDB DOI: https://doi.org/10.2210/pdb3VNO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingomonas paucimobilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-17 Released: 2013-02-06 
• Deposition Author(s): Fujishiro, T., Shoji, O., Sugimoto, H., Shiro, Y., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.227 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

A substrate-binding-state mimic of H2O2-dependent cytochrome P450 produced by one-point mutagenesis and peroxygenation of non-native substrates

Shoji, O., Fujishiro, T., Nishio, K., Kano, Y., Kimoto, H., Chien, S.-C., Onoda, H., Muramatsu, A., Tanaka, S., Hori, A., Sugimoto, H., Shiro, Y., Watanabe, Y.

(2016) Catal Sci Technol 6: 5806-5811

• DOI: https://doi.org/10.1039/C6CY00630B

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: 46.33 kDa 
• Atom Count: 3,359 
• Modelled Residue Count: 407 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid alpha-hydroxylase	A	407	Sphingomonas paucimobilis	Mutation(s): 1  EC: 1.11.2.4
UniProt
Find proteins for O24782 (Sphingomonas paucimobilis) Explore O24782  Go to UniProtKB:  O24782

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.227 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.539	α = 90
b = 94.539	β = 90
c = 113.004	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Fujishiro, T., Shoji, O., Sugimoto, H., Shiro, Y., Watanabe, Y.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description