Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40340.05 
• Atom Count: 2659 
• Residue Count: 335 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

6GED

Adhesin domain of PrgB from Enterococcus faecalis bound to DNA

• DOI: 10.2210/pdb6GED/pdb

• Classification: CELL ADHESION
• Organism(s): synthetic construct, Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2018-04-26 Released: 2018-05-16 
• Deposition Author(s): Schmitt, A., Berntsson, R.P.A.
• Funding Organization(s): Swedish Research Council; Kempestiftelserna 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.794 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 

Literature

PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.

Schmitt, A., Jiang, K., Camacho, M.I., Jonna, V.R., Hofer, A., Westerlund, F., Christie, P.J., Berntsson, R.P.

(2018) Mol. Microbiol. 109: 291-305

• PubMed: 29723434 
• Primary Citation of Related Structures:  
  6EVU

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PrgB	A	315	Enterococcus faecalis	Mutation(s): 0  Gene Names: prgB
Find proteins for Q04112 (Enterococcus faecalis) Go to UniProtKB:  Q04112

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')	C	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')	D	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.794 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 32.017	α = 90.00
b = 93.026	β = 90.00
c = 99.097	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
PHASER	phasing
XSCALE	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-04-26 
• Released Date: 2018-05-16 
• Deposition Author(s): Schmitt, A., Berntsson, R.P.A.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03599
Kempestiftelserna	Sweden	JCK-1524

Revision History 

• Version 1.0: 2018-05-16
  Type: Initial release
• Version 1.1: 2018-10-03
  Type: Data collection, Database references