7Y9M

Crystal structure of P450 BM3-2F from Bacillus megaterium

• PDB DOI: https://doi.org/10.2210/pdb7Y9M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-25 Released: 2023-07-12 
• Deposition Author(s): Wang, Q., Zhang, L.L., Liu, W.D., Huang, J.-W., Yang, Y., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Crystal structure of P450 BM3-2F from Bacillus megaterium

Wang, Q., Zhang, L.L., Liu, W.D., Huang, J.-W., Yang, Y., Chen, C.-C., Guo, R.-T.

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: 106.18 kDa 
• Atom Count: 7,646 
• Modelled Residue Count: 878 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	457	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 2  Gene Names: cyp102A1, cyp102, BG04_163 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
IMD	D [auth A], F [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.767	α = 90
b = 146.357	β = 97.28
c = 62.891	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Wang, Q., Zhang, L.L., Liu, W.D., Huang, J.-W., Yang, Y., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description