5M31 Antitoxin date Oct 13, 2016
title Macrodomain Of Thermus Aquaticus Darg
authors A.Ariza
compound source
Molecule: Appr-1-P Processing Domain Protein
Chain: A
Engineered: Yes
 Organism_scientific: Thermus Aquaticus Y51mc23
Organism_taxid: 498848
Gene: Taqdraft_4250
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta
Expression_system_vector_type: Pet28a
symmetry Space Group: C 1 2 1
R_factor 0.172 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.600 45.020 35.540 90.00 101.25 90.00
method X-Ray Diffractionresolution 1.67 Å
ligand CL, GOL enzyme
Gene TAQDRAFT
Primary referenceThe Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA., Jankevicius G, Ariza A, Ahel M, Ahel I, Mol Cell. 2016 Dec 15;64(6):1109-1116. doi: 10.1016/j.molcel.2016.11.014. Epub, 2016 Dec 8. PMID:27939941
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (5m31.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 5M31
  • CSU: Contacts of Structural Units for 5M31
  • Structure Factors (405 Kb)
  • Retrieve 5M31 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M31 from S2C, [Save to disk]
  • Re-refined 5m31 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5M31 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 5M31
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5m31] [5m31_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5M31
  • Community annotation for 5M31 at PDBWiki (http://pdbwiki.org)

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