7XZK

Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-pipecolyl-L-phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb7XZK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-02 Released: 2023-06-07 
• Deposition Author(s): Shoji, O., Yonemura, K.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-pipecolyl-L-phenylalanine

Ariyasu, S., Yonemura, K., Kasai, C., Aiba, Y., Onoda, H., Shisaka, Y., Sugimoto, H., Tosha, T., Kubo, M., Kamachi, T., Yoshizawa, K., Shoji, O.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.66 kDa 
• Atom Count: 8,103 
• Modelled Residue Count: 906 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	456	Priestia megaterium	Mutation(s): 0  Gene Names: cyp102A1 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
I8F (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2~{S})-2-[[(2~{S})-1-(3-cyclohexylpropanoyl)piperidin-2-yl]carbonylamino]-3-phenyl-propanoic acid C24 H34 N2 O4 XVAOXPXEZULIIX-SFTDATJTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.966	α = 90
b = 145.581	β = 97.03
c = 63.133	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Shoji, O., Yonemura, K.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR15P3

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description