5YHF Membrane Protein date Sep 28, 2017
title Crystal Structure Of Secdf In Super-Membrane-Facing Form
authors Y.Tanaka, T.Tsukazaki, K.Yoshikaie, A.Furukawa
compound source
Molecule: Protein Translocase Subunit Secdf
Chain: A
Engineered: Yes
Mutation: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Secdf, Ttha0697
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 1
R_factor 0.203 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.190 65.640 79.980 75.11 75.23 80.83
method X-Ray Diffractionresolution 2.80 Å
ligand OLC, PEG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRemote Coupled Drastic beta-Barrel to beta-Sheet Transition of the Protein Translocation Motor., Furukawa A, Nakayama S, Yoshikaie K, Tanaka Y, Tsukazaki T, Structure. 2018 Jan 26. pii: S0969-2126(18)30002-9. doi:, 10.1016/j.str.2018.01.002. PMID:29398525
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (5yhf.pdb1.gz) 230 Kb
  • LPC: Ligand-Protein Contacts for 5YHF
  • CSU: Contacts of Structural Units for 5YHF
  • Structure Factors (234 Kb)
  • Retrieve 5YHF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YHF from S2C, [Save to disk]
    • View 5YHF 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 5YHF
  • 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: [5yhf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5YHF
  • Community annotation for 5YHF at PDBWiki (http://pdbwiki.org)

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