7V40 | pdb_00007v40

Crystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2

PDB DOI: https://doi.org/10.2210/pdb7V40/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.175 (Depositor), 0.178 (DCC)
R-Value Work:
0.151 (Depositor), 0.158 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 50.12 kDa
Atom Count: 4,209
Modeled Residue Count: 432
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A088FL33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.175 (Depositor), 0.178 (DCC)
R-Value Work: 0.151 (Depositor), 0.158 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.092	α = 90
b = 111.092	β = 90
c = 80.815	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.