4KDP

TcaR-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the MarR family proteins

Structural Biology Knowledgebase: 4KDP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.274

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KDP

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 132948.00


Macromolecule Entities
Molecule Chains Length Organism Details
TcaR transcription regulator A, B, C..., D, E, F, GA, B, C, D, E, F, G 151 Staphylococcus epidermidis Gene Name(s): SE_1937
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3') H, J 17 synthetic

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

B, F, H, J 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B, E, F, H 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.274
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.90 α = 90.00
b = 91.90 β = 90.00
c = 261.53 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-25
  • Released Date: 2014-03-19
  • Deposition author(s): Chang, Y.M., Chen, C.K.-M., Wang, A.H.-J.

Revision History

  • 2014-05-14
    Type: Citation | Details: Citation update