5APG Transferase date Sep 15, 2015
title Structure Of The Sam-Dependent Rrna:Acp-Transferase Tsr3 From Vulcanisaeta Distributa
authors J.P.Wurm, C.Immer, D.Pogoryelov, B.Meyer, P.Koetter, K.D.Entian, J.Woehnert
compound source
Molecule: Tsr3
Chain: A, B, C
Ec: 2.5.1.-
Engineered: Yes
Other_details: Containing Selenomethionine Instead Of Methi
Organism_scientific: Vulcanisaeta Distributa
Organism_taxid: 572478
Strain: Dsm 14429
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet11
symmetry Space Group: C 1 2 1
R_factor 0.1927 R_Free 0.2030
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.950 66.970 106.420 90.00 89.99 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EEM, MES, MSE enzyme Transferase E.C.2.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceRibosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans., Meyer B, Wurm JP, Sharma S, Immer C, Pogoryelov D, Kotter P, Lafontaine DL, Wohnert J, Entian KD, Nucleic Acids Res. 2016 Apr 15. pii: gkw244. PMID:27084949
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (5apg.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (5apg.pdb2.gz) 36 Kb
  • Biological Unit Coordinates (5apg.pdb3.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 5APG
  • CSU: Contacts of Structural Units for 5APG
  • Structure Factors (1697 Kb)
  • Retrieve 5APG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5APG from S2C, [Save to disk]
  • Re-refined 5apg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5APG 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 5APG
  • 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: [5apg_B] [5apg] [5apg_C] [5apg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5APG
  • Community annotation for 5APG at PDBWiki (http://pdbwiki.org)

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