5Y0O Ligase date Jul 18, 2017
title Crystal Structure Of Apo Bstmcal
authors S.Yamashita, K.Tomita
compound source
Molecule: Upf0348 Protein B4417_3650
Chain: A, B
Engineered: Yes
Other_details: The Gene Was Cloned Into Pet15b With Ndei An Site, And Expressed As A N-Terminally His-Tagged Protein.
 Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: B4417_3650
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.755 67.656 210.805 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAcetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis., Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, Suzuki T, Nat Chem Biol. 2018 Nov;14(11):1010-1020. doi: 10.1038/s41589-018-0119-z. Epub, 2018 Aug 27. PMID:30150682
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (284 Kb) [Save to disk]
  • Biological Unit Coordinates (5y0o.pdb1.gz) 278 Kb
  • CSU: Contacts of Structural Units for 5Y0O
  • Structure Factors (355 Kb)
  • Retrieve 5Y0O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y0O from S2C, [Save to disk]
    • View 5Y0O 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 5Y0O
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y0o_A] [5y0o_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Y0O
  • Community annotation for 5Y0O at PDBWiki (http://pdbwiki.org)

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