7Y9J | pdb_00007y9j

Crystal structure of P450 BM3-TMK from Bacillus megaterium in complex with 5-nitro-1,2-benzisoxazole

• PDB DOI: https://doi.org/10.2210/pdb7Y9J/pdb

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


• Deposited: 2022-06-24 Released: 2023-06-28 
• 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: 1.83 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Engineering of a P450-based Kemp eliminase with a new mechanism

Li, A., Wang, Q., Song, X., Zhang, X., Huang, J.W., Chen, C.C., Guo, R.T., Wang, B., Reetz, M.T.

(2023) Chinese J Catal 47: 191-199

• DOI: https://doi.org/10.1016/S1872-2067(23)64389-X

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: 107.42 kDa 
• Atom Count: 7,929 
• Modeled Residue Count: 902 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	465	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 4  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], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
H5J (Subject of Investigation/LOI)	E [auth B]	5-nitro-1,2-benzoxazole C7 H4 N2 O3 TWOYWCWKYDYTIP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.767	α = 90
b = 146.73	β = 97.71
c = 63.587	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
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: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description