3I8P

Crystal structure of E. coli FabF(C163A) in complex with Platensimycin A1

• PDB DOI: https://doi.org/10.2210/pdb3I8P/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-09 Released: 2010-07-28 
• Deposition Author(s): Soisson, S.M., Parthsarathy, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.182 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Isolation, enzyme-bound structure and antibacterial activity of platencin A1 from Streptomyces platensis.

Singh, S.B., Ondeyka, J.G., Herath, K.B., Zhang, C., Jayasuriya, H., Zink, D.L., Parthasarathy, G., Becker, J.W., Wang, J., Soisson, S.M.

(2009) Bioorg Med Chem Lett 19: 4756-4759

• PubMed: 19581087 
• DOI: https://doi.org/10.1016/j.bmcl.2009.06.061
• Primary Citation of Related Structures:  
  3HNZ, 3HO2, 3HO9, 3I8P


• PubMed Abstract: 
  

  Natural products continue to serve as one of the best sources for discovery of antibacterial agents as exemplified by the recent discoveries of platensimycin and platencin. Chemical modifications as well as discovery of congeners are the main sources for gaining knowledge of structure-activity relationship of natural products. Screening for congeners in the extracts of the fermentation broths of Streptomyces platensis led to the isolation of platencin A(1), a hydroxy congener of platencin. The hydroxylation of the tricyclic enone moiety negatively affected the antibacterial activity and appears to be consistent with the hydrophobic binding pocket of the FabF. Isolation, structure, enzyme-bound structure and activity of platencin A(1) and two other congeners have been described.

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Organizational Affiliation: 

Merck Research Laboratories, Rahway, NJ 07065, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.06 kDa 
• Atom Count: 3,575 
• Modelled Residue Count: 411 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A	427	Escherichia coli K-12	Mutation(s): 1  Gene Names: fabF, fabJ, b1095, JW1081 EC: 2.3.1.179
UniProt
Find proteins for P0AAI5 (Escherichia coli (strain K12)) Explore P0AAI5  Go to UniProtKB:  P0AAI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
840	B [auth A]	Platensimycin A1 C24 H25 N O8 TUHIUIGYYSZKCN-ACYPNERUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.182 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.016	α = 90
b = 76.016	β = 90
c = 144.941	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Soisson, S.M., Parthsarathy, G.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description