6JFD

K1U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6JFD/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-08 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: 2.40 Å
• R-Value Free: 0.283 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

Literature

K1U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa

Lee, I.H., Ho, T.H., Kang, L.W.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.58 kDa 
• Atom Count: 5,100 
• Modelled Residue Count: 639 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	168	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.1.88
UniProt
Find proteins for A0A071LDC0 (Pseudomonas aeruginosa) Explore A0A071LDC0  Go to UniProtKB:  A0A071LDC0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K1U (Subject of Investigation/LOI)	I [auth C]	(3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid C19 H18 O4 S XBDWLLDIBQGWMW-MRXNPFEDSA-N
NI	E [auth A], F [auth B], G [auth B], H [auth C], J [auth D], K [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.283 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.33	α = 90
b = 146.356	β = 109.9
c = 65.306	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