5X11 Transcription Dna date Jan 24, 2017
title Crystal Structure Of Bacillus Subtilis Padr In Complex With Dna
authors S.C.Park, Y.M.Kwak, W.S.Song, M.Hong, S.I.Yoon
compound source
Molecule: Dna (28-Mer)
Chain: I, M
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (28-Mer)
Chain: J, N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcriptional Regulator
Chain: A, B, C, D, E, F, G, H
Engineered: Yes

Organism_scientific: Bacillus Subtilis Subsp. Spizizenii St
Organism_taxid: 655816
Strain: W23
Gene: Padr, Bsuw23_04210
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.228 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
341.807 61.567 120.553 90.00 107.94 90.00
method X-Ray Diffractionresolution 2.65 Å
Primary referenceStructural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR., Park SC, Kwak YM, Song WS, Hong M, Yoon SI, Nucleic Acids Res. 2017 Nov 9. pii: 4607799. doi: 10.1093/nar/gkx1055. PMID:29136175
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (579 Kb) [Save to disk]
  • Biological Unit Coordinates (5x11.pdb1.gz) 169 Kb
  • Biological Unit Coordinates (5x11.pdb2.gz) 169 Kb
  • Biological Unit Coordinates (5x11.pdb3.gz) 121 Kb
  • Biological Unit Coordinates (5x11.pdb4.gz) 117 Kb
  • CSU: Contacts of Structural Units for 5X11
  • Structure Factors (1088 Kb)
  • Retrieve 5X11 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X11 from S2C, [Save to disk]
  • View 5X11 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5X11
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5x11 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x11_D] [5x11_F] [5x11_N] [5x11_J] [5x11_B] [5x11_E] [5x11_I] [5x11_H] [5x11_A] [5x11_C] [5x11_G] [5x11_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X11
  • Community annotation for 5X11 at PDBWiki (http://pdbwiki.org)

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