6DCD

Mycobacterium marinum cytochrome P450 CYP150A6 in the substrate-free form

PDB DOI: https://doi.org/10.2210/pdb6DCD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium marinum M
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-05-05 Released: 2019-03-20
Deposition Author(s): Child, S.A., Bruning, J.B., Bell, S.G.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.246
R-Value Work: 0.222
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum.

Child, S.A., Flint, K.L., Bruning, J.B., Bell, S.G.

(2019) Biochim Biophys Acta Gen Subj 1863: 925-934

PubMed: 30826435 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2019.02.016
Primary Citation of Related Structures:
6DCD

PubMed Abstract:
Actinobacteria, including the Mycobacteria, have a large component of cytochrome P450 family monooxygenases. This includes Mycobacterium tuberculosis, M. ulcerans and M. marinum, and M. vanbaalenii. These enzymes can abstract CH bonds and have important roles in natural product biosynthesis.

Organizational Affiliation

Department of Chemistry, University of Adelaide, SA 5005, Australia.

Macromolecule Content

Total Structure Weight: 48.4 kDa
Atom Count: 3,759
Modelled Residue Count: 406
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 150A6 Cyp150A6	A	424	Mycobacterium marinum M	Mutation(s): 0 Gene Names: cyp150A6, MMAR_4694
UniProt
Find proteins for B2HFD6 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HFD6 Go to UniProtKB: B2HFD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2HFD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.246
R-Value Work: 0.222
R-Value Observed: 0.223
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.57	α = 90
b = 80.57	β = 90
c = 134.76	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT140100355

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2019-03-27
Changes: Data collection, Database references
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.