5JQF Unknown Function date May 04, 2016
title Crystal Structure Of The Lasso Peptide Sphingopyxin I (Spi)
authors C.D.Fage, J.D.Hegemann, K.Harms, G.Bange, M.A.Marahiel
compound source
Molecule: Sphingopyxin I
Chain: A, B
Engineered: Yes
Other_details: An Isopeptide Bond Exists Between The N-Term Gly1 And Side Chain Of Asp9
 Organism_scientific: Sphingopyxis Alaskensis Rb2256
Organism_taxid: 317655
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet41a
symmetry Space Group: P 65
R_factor 0.129 R_Free 0.153
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.240 39.240 31.410 90.00 90.00 120.00
method X-Ray Diffractionresolution 0.85 Å
Primary referenceStructure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase., Fage CD, Hegemann JD, Nebel AJ, Steinbach RM, Zhu S, Linne U, Harms K, Bange G, Marahiel MA, Angew Chem Int Ed Engl. 2016 Oct 4;55(41):12717-21. doi: 10.1002/anie.201605232. , Epub 2016 Sep 9. PMID:27611791
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (5jqf.pdb1.gz) 14 Kb
  • Biological Unit Coordinates (5jqf.pdb2.gz) 12 Kb
  • CSU: Contacts of Structural Units for 5JQF
  • Structure Factors (209 Kb)
  • Retrieve 5JQF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JQF from S2C, [Save to disk]
  • Re-refined 5jqf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JQF 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 5JQF
  • 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: [5jqf_B] [5jqf] [5jqf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JQF
  • Community annotation for 5JQF at PDBWiki (http://pdbwiki.org)

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