7V45 | pdb_00007v45

Crystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with para-bromotoluene.

• PDB DOI: https://doi.org/10.2210/pdb7V45/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rhodococcus coprophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-12 Released: 2022-06-22 
• Deposition Author(s): Zhang, L.L., Huang, J.W., Liu, W.D., Chen, C.C., Guo, R.T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis for a Toluene Monooxygenase to Govern Substrate Selectivity

Chen, C.C., Dai, M., Zhang, L., Zhao, J., Zeng, W., Shi, M., Huang, J.W., Liu, W., Guo, R.T., Li, A.

(2022) ACS Catal 12: 2831-2839

• DOI: https://doi.org/10.1021/acscatal.1c05845

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: 50.29 kDa 
• Atom Count: 4,224 
• Modeled Residue Count: 431 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p450tol monooxygenase	A	440	Rhodococcus coprophilus	Mutation(s): 0
UniProt
Find proteins for A0A088FL33 (Rhodococcus coprophilus) Explore A0A088FL33  Go to UniProtKB:  A0A088FL33

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
C5O (Subject of Investigation/LOI)	B [auth A]	1-bromanyl-4-methyl-benzene C7 H7 Br ZBTMRBYMKUEVEU-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.036	α = 90
b = 111.036	β = 90
c = 80.708	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Zhang, L.L., Huang, J.W., Liu, W.D., Chen, C.C., Guo, R.T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Structure summary
• Version 1.2: 2023-11-29
  Changes: Refinement description