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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

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

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.