2W7Z

Structure of the pentapeptide repeat protein EfsQnr, a DNA gyrase inhibitor. Free amines modified by cyclic pentylation with glutaraldehyde.

• PDB DOI: https://doi.org/10.2210/pdb2W7Z/pdb

• Classification: INHIBITOR
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-06 Released: 2009-05-05 
• Deposition Author(s): Vetting, M.W., Hegde, S.S., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Crystallization of a Pentapeptide-Repeat Protein by Reductive Cyclic Pentylation of Free Amines with Glutaraldehyde.

Vetting, M.W., Hegde, S.S., Blanchard, J.S.

(2009) Acta Crystallogr D Biol Crystallogr 65: 462

• PubMed: 19390151 
• DOI: https://doi.org/10.1107/S0907444909008324
• Primary Citation of Related Structures:  
  2W7Z


• PubMed Abstract: 
  

  The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane-dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 A resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 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 PQS (software)

Macromolecule Content

• Total Structure Weight: 50.19 kDa 
• Atom Count: 3,910 
• Modelled Residue Count: 415 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENTAPEPTIDE REPEAT FAMILY PROTEIN	A, B	214	Enterococcus faecalis	Mutation(s): 0
UniProt
Find proteins for Q837D8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837D8  Go to UniProtKB:  Q837D8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LP6	A, B	L-PEPTIDE LINKING	C11 H22 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.93	α = 90
b = 63.139	β = 96.09
c = 94.619	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Vetting, M.W., Hegde, S.S., Blanchard, J.S.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary