8A8L

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment

• PDB DOI: https://doi.org/10.2210/pdb8A8L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-23 Released: 2023-07-05 
• Deposition Author(s): Snee, M., Katariya, M., Levy, C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment

Snee, M., Katariya, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.07 kDa 
• Atom Count: 3,616 
• Modelled Residue Count: 393 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 protein	A	400	Staphylococcus aureus	Mutation(s): 0  Gene Names: cypX_1, NCTC5664_01270, cypX EC: 1.14.15.13
UniProt
Find proteins for A0A380DQV1 (Staphylococcus aureus) Explore A0A380DQV1  Go to UniProtKB:  A0A380DQV1

Small Molecules

Ligands 4 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
LBJ (Subject of Investigation/LOI)	G [auth A]	6-methoxy-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole C12 H14 N2 O QYMDEOQLJUUNOF-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	C [auth A], E [auth A], F [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.77	α = 90
b = 108.169	β = 90
c = 105.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Snee, M., Katariya, M., Levy, C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description