6JFO | pdb_00006jfo

Formyl-Met-Ala-Ser bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb6JFO/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus, Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-11 Released: 2020-02-12 
• Deposition Author(s): Lee, I.H., Ho, T.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Formyl-Met-Ala-Ser bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

Lee, I.H., Ho, T.H., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 20.98 kDa 
• Atom Count: 1,633 
• Modeled Residue Count: 186 
• Deposited Residue Count: 186 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	183	Staphylococcus aureus	Mutation(s): 0  Gene Names: def, def1, pdf1 EC: 3.5.1.88
UniProt
Find proteins for P68826 (Staphylococcus aureus) Explore P68826  Go to UniProtKB:  P68826

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FME-ALA-SER	B	3	Arabidopsis thaliana	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
FME	B	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.733	α = 90
b = 120.831	β = 90
c = 47.393	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Lee, I.H., Ho, T.H., Kang, L.W.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary