3K6L | pdb_00003k6l

The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827

• PDB DOI: https://doi.org/10.2210/pdb3K6L/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-09 Released: 2009-11-10 
• Deposition Author(s): Cheng, R.K.Y., Crawley, L., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.319 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827

Cheng, R.K.Y., Crawley, L., Wood, M., Barker, J., Felicetti, B., Whittaker, 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 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)

Macromolecule Content 

• Total Structure Weight: 58.94 kDa 
• Atom Count: 4,138 
• Modeled Residue Count: 481 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C	169	Escherichia coli K-12	Mutation(s): 0  Gene Names: def, fms, b3287, JW3248 EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3  Go to UniProtKB:  P0A6K3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BB	E [auth A], G [auth B]	(2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide C16 H31 N3 O5 USHCFFHZEHRVBD-GRYCIOLGSA-N
NI	D [auth A], F [auth B], H [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.319 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.96	α = 90
b = 73.96	β = 90
c = 241.5	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Cheng, R.K.Y., Crawley, L., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description