8AE8 | pdb_00008ae8

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

• PDB DOI: https://doi.org/10.2210/pdb8AE8/pdb

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


• Deposited: 2022-07-12 Released: 2023-08-16 
• Deposition Author(s): Snee, M., Katariya, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.74 kDa 
• Atom Count: 3,412 
• Modeled Residue Count: 391 
• 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 (PDB Primary Data), 1.14 (UniProt)
UniProt
Find proteins for A0A380DQV1 (Staphylococcus aureus) Explore A0A380DQV1  Go to UniProtKB:  A0A380DQV1

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
LUU (Subject of Investigation/LOI)	C [auth A]	1~{H}-indol-5-ylmethanamine C9 H10 N2 UAYYSAPJTRVEQA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.889	α = 90
b = 107.841	β = 90
c = 105.695	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: 2023-08-16 
Deposition Author(s): Snee, M., Katariya, M.

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

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release