5DDG

The structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with target double strand DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 5DDG

Classification: TRANSCRIPTION REGULATOR / DNA

Total Structure Weight: 70135.18


Macromolecule Entities
Molecule Chains Length Organism Details
transcriptional factor AraR A, B 228 Bacteroides thetaiotaomicron Gene Name(s): BT_0354
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (27-MER) C 27 Bacteroides thetaiotaomicron
DNA (27-MER) D 27 Bacteroides thetaiotaomicron

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MLA
Query on MLA

A, B MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID (Synonym)
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.200
  • Space Group: P 2 3

Unit Cell:

Length (Å) Angle (°)
a = 163.02 α = 90.00
b = 163.02 β = 90.00
c = 163.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-08-24
  • Released Date: 2015-09-09
  • Deposition author(s): Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2015-10-21
    Type: Database references
  • 2015-12-16
    Type: Database references