7OW9 | pdb_00007ow9

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with Cyclo-L-leucyl-L-leucine

• PDB DOI: https://doi.org/10.2210/pdb7OW9/pdb

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


• Deposited: 2021-06-17 Released: 2021-08-25 
• Deposition Author(s): Snee, M., Levy, C., Leys, D., Katariya, M., Munro, A.W.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with Cyclo-L-leucyl-L-leucine

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: 46.88 kDa 
• Atom Count: 3,580 
• Modeled Residue Count: 393 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYPX	A	400	Staphylococcus aureus	Mutation(s): 0  EC: 1.14
UniProt
Find proteins for A0A380DQV1 (Staphylococcus aureus) Explore A0A380DQV1  Go to UniProtKB:  A0A380DQV1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
2IO (Subject of Investigation/LOI)	B [auth A]	(3S,6S)-3,6-bis(2-methylpropyl)piperazine-2,5-dione C12 H22 N2 O2 XWYXUMDVQIOAPR-UWVGGRQHSA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.179	α = 90
b = 105.025	β = 90
c = 104.219	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Snee, M., Levy, C., Leys, D., Katariya, M., Munro, A.W.

---

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

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 2.0: 2021-09-29
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description