6CVC | pdb_00006cvc

Mycobacterium marinum cytochrome P450 CYP124A1 in the substrate-free form

• PDB DOI: https://doi.org/10.2210/pdb6CVC/pdb

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


• Deposited: 2018-03-27 Released: 2019-03-27 
• Deposition Author(s): Child, S.A., Bruning, J.B., Bell, S.G.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

A comparison of the steroid binding cytochrome P450s from Mycobacterium marinum and Mycobacterium tuberculosis

Child, S.A., Bruning, J.B., Bell, S.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.37 kDa 
• Atom Count: 3,718 
• Modeled Residue Count: 422 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 124A1, Cyp124A1	A	433	Mycobacterium marinum M	Mutation(s): 0  Gene Names: cyp124A1, MMAR_3361
UniProt
Find proteins for B2HHT9 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HHT9  Go to UniProtKB:  B2HHT9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.776	α = 90
b = 72.359	β = 109.72
c = 65.602	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Child, S.A., Bruning, J.B., Bell, S.G.

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

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description