6L8E Antitoxin Toxin Dna date Nov 06, 2019
title Crystal Structure Of Heterohexameric Yoeb-Yefm Complex Bound Dna
authors J.Yue, L.Xue
compound source
Molecule: Yefm Antitoxin
Chain: A, B, C, D, I, J, K, L
Engineered: Yes
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061
Strain: Nctc 8325
Gene: Saouhsc_02692
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Yoeb Toxin
Chain: E, F, M, N
Engineered: Yes

Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061
Strain: Nctc 8325
Gene: Saouhsc_02691
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (26-Mer)
Chain: G, O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (26-Mer)
Chain: H, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.197 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
151.352 151.352 183.778 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
Gene
Ontology
ChainFunctionProcessComponent
F, M, N, E
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity, p...


  • Primary referenceDistinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system., Xue L, Yue J, Ke J, Khan MH, Wen W, Sun B, Zhu Z, Niu L, Nucleic Acids Res. 2020 Aug 26. pii: 5897335. doi: 10.1093/nar/gkaa706. PMID:32845304
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (197 Kb) [Save to disk]
  • Biological Unit Coordinates (6l8e.pdb1.gz) 95 Kb
  • Biological Unit Coordinates (6l8e.pdb2.gz) 96 Kb
  • CSU: Contacts of Structural Units for 6L8E
  • Structure Factors (2503 Kb)
  • Retrieve 6L8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6L8E from S2C, [Save to disk]
  • View 6L8E 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 6L8E
  • 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 6l8e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6l8e_B] [6l8e_M] [6l8e_F] [6l8e_H] [6l8e_N] [6l8e_C] [6l8e_G] [6l8e_E] [6l8e_D] [6l8e_I] [6l8e_L] [6l8e_P] [6l8e_A] [6l8e_J] [6l8e_O] [6l8e_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6L8E
  • Community annotation for 6L8E at PDBWiki (http://pdbwiki.org)

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