1IX1

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

• PDB DOI: https://doi.org/10.2210/pdb1IX1/pdb

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


• Deposited: 2002-06-07 Released: 2003-09-09 
• Deposition Author(s): Kim, H.-W., Yoon, H.-J., Lee, J.Y., Han, B.W., Yang, J.K., Lee, B.I., Ahn, H.J., Lee, H.H., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent

Yoon, H.-J., Kim, H.L., Lee, S.K., Kim, H.-W., Kim, H.-W., Lee, J.Y., Mikami, B., Suh, S.W.

(2004) Proteins 57: 639-642

• PubMed: 15382235 
• DOI: https://doi.org/10.1002/prot.20231
• Primary Citation of Related Structures:  
  1IX1, 1Q1Y

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.89 kDa 
• Atom Count: 3,106 
• Modelled Residue Count: 338 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide deformylase	A, B	171	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.1.88
UniProt
Find proteins for Q9I7A8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7A8  Go to UniProtKB:  Q9I7A8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	D [auth A], G [auth B]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
MHA	E [auth A], H [auth B]	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID C6 H10 N2 O5 QZTKDVCDBIDYMD-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.75	α = 90
b = 74.46	β = 90
c = 77.18	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Kim, H.-W., Yoon, H.-J., Lee, J.Y., Han, B.W., Yang, J.K., Lee, B.I., Ahn, H.J., Lee, H.H., Suh, S.W.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations