3WVF Chaperone date May 20, 2014
title Crystal Structure Of Yidc From Escherichia Coli
authors K.Kumazaki, T.Tsukazaki, T.Kishimoto, R.Ishitani, O.Nureki
compound source
Molecule: Membrane Protein Insertase Yidc
Chain: A, B
Fragment: Unp Residues 1-540
Synonym: Foldase Yidc, Membrane Integrase Yidc, Membrane Pr Yidc;
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 364106
Strain: Uti89
Gene: Yidc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet Variant
symmetry Space Group: P 1
R_factor 0.221 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.729 76.011 91.318 78.08 82.45 77.55
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • membrane insertase activity


  • Primary referenceCrystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase., Kumazaki K, Kishimoto T, Furukawa A, Mori H, Tanaka Y, Dohmae N, Ishitani R, Tsukazaki T, Nureki O, Sci Rep. 2014 Dec 3;4:7299. doi: 10.1038/srep07299. PMID:25466392
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (3wvf.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (3wvf.pdb2.gz) 70 Kb
  • CSU: Contacts of Structural Units for 3WVF
  • Structure Factors (141 Kb)
  • Retrieve 3WVF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WVF from S2C, [Save to disk]
  • Re-refined 3wvf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WVF 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 3WVF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3WVF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wvf] [3wvf_A] [3wvf_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3WVF
  • Community annotation for 3WVF at PDBWiki (http://pdbwiki.org)

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