6GED

Adhesin domain of PrgB from Enterococcus faecalis bound to DNA


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PrgB
A
315Enterococcus faecalisMutation(s): 0 
Gene Names: prgB
Find proteins for Q04112 (Enterococcus faecalis)
Go to UniProtKB:  Q04112
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')C10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')D10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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 = 32.017α = 90.00
b = 93.026β = 90.00
c = 99.097γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03599
KempestiftelsernaSwedenJCK-1524

Revision History 

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