Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50188.53 
• Atom Count: 3493 
• Residue Count: 428 
• Unique protein chains: 1

2W7Z

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

• DOI: 10.2210/pdb2W7Z/pdb

• Classification: INHIBITOR
• Organism(s): Enterococcus faecalis (strain ATCC 700802 / V583)
• Expression System: Escherichia coli


• 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: 1.6 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 

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.,Sect.D 65: 462

• PubMed: 19390151 
• DOI: 10.1107/S0907444909008324


• 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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, 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: 1.6 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 36.930	α = 90.00
b = 63.139	β = 96.09
c = 94.619	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-06 
• 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
  Type: Advisory, Version format compliance