8Q5J | pdb_00008q5j

Cytochrome P450 monooxygenase from Streptomyces scabiei (SscaCYP)

PDB DOI: https://doi.org/10.2210/pdb8Q5J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces scabiei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-09 Released: 2024-04-03
Deposition Author(s): Opperman, D.J., Ebrecht, A.C.
Funding Organization(s): Other government, Global Challenges Research Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.189 (Depositor), 0.187 (DCC)
R-Value Work:
0.164 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Natural alternative heme-environments allow efficient peroxygenase activity by cytochrome P450 monooxygenases

Ebrecht, A.C., Smit, M.S., Opperman, D.J.

(2023) Catal Sci Technol 13: 6264-6273

DOI: https://doi.org/10.1039/D3CY01207G

Macromolecule Content

Total Structure Weight: 44.94 kDa
Atom Count: 3,419
Modeled Residue Count: 386
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 107B1	A	398	Streptomyces scabiei	Mutation(s): 0 Gene Names: SsS58_05869
UniProt
Find proteins for A0A100JTL7 (Streptomyces scabiei) Explore A0A100JTL7 Go to UniProtKB: A0A100JTL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A100JTL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM 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]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.189 (Depositor), 0.187 (DCC)
R-Value Work: 0.164 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.27	α = 90
b = 46.89	β = 90
c = 75.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
xia2	data reduction
BALBES	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		IBH-UFS
Global Challenges Research Fund	United Kingdom	ST/R002754/1

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release
Version 1.1: 2025-02-26
Changes: Structure summary

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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.