5X6E Dna Binding Protein Dna date Feb 21, 2017
title Crystal Structure Of Prfa-Dna Binary Complex
authors Y.Wang, H.Feng, Y.L.Zhu, P.Gao
compound source
Molecule: Listeriolysin Positive Regulatory Factor A
Chain: M, N, A, B, E, F
Synonym: Listeriolysin Positive Regulatory Protein,Listerio Regulatory Protein,Pleitrophic Regulatory Factor A,Positive Regulatory Factor A,Prfa,Transcriptional Regulator;
Engineered: Yes
Organism_scientific: Listeria Monocytogenes
Organism_taxid: 1639
Gene: Prfa, Ajl40_05990, Ajn46_04535, M643_11230
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (29-Mer)
Chain: O, C, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Listeria Monocytogenes
Organism_taxid: 1639

Molecule: Dna (28-Mer)
Chain: P, D, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Listeria Monocytogenes
Organism_taxid: 1639
symmetry Space Group: P 21 21 21
R_factor 0.249 R_Free 0.300
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.017 96.590 370.528 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.99 Å
ligand GSH enzyme
Gene AJL40 ; AJN46 ; M643
Gene
Ontology
ChainFunctionProcessComponent
F, A, M, N, E, B


Primary referenceStructural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes., Wang Y, Feng H, Zhu Y, Gao P, Protein Cell. 2017 Apr;8(4):308-312. doi: 10.1007/s13238-017-0390-x. PMID:28271443
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (315 Kb) [Save to disk]
  • Biological Unit Coordinates (5x6e.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (5x6e.pdb2.gz) 106 Kb
  • Biological Unit Coordinates (5x6e.pdb3.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 5X6E
  • CSU: Contacts of Structural Units for 5X6E
  • Structure Factors (741 Kb)
  • Retrieve 5X6E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X6E from S2C, [Save to disk]
  • Re-refined 5x6e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5X6E 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 5X6E
  • 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 5x6e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x6e_H] [5x6e_M] [5x6e_N] [5x6e_D] [5x6e] [5x6e_G] [5x6e_F] [5x6e_P] [5x6e_C] [5x6e_E] [5x6e_A] [5x6e_O] [5x6e_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X6E
  • Community annotation for 5X6E at PDBWiki (http://pdbwiki.org)

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