4YZI Crystal structure of blue-shifted channelrhodopsin mutant (T198G/G202A) date
authors Kato, H.E., Kamiya, M., Ishitani, R., Hayashi, S., Nureki, O.
compound source
symmetry
R_factor
R_Free 0.2410
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand OLA, RET, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAtomistic design of microbial opsin-based blue-shifted optogenetics tools., Kato HE, Kamiya M, Sugo S, Ito J, Taniguchi R, Orito A, Hirata K, Inutsuka A, Yamanaka A, Maturana AD, Ishitani R, Sudo Y, Hayashi S, Nureki O, Nat Commun. 2015 May 15;6:7177. doi: 10.1038/ncomms8177. PMID:25975962
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (4yzi.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 4YZI
  • CSU: Contacts of Structural Units for 4YZI
  • Structure Factors (350 Kb)
  • Retrieve 4YZI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YZI from S2C, [Save to disk]
  • Re-refined 4yzi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YZI 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 4YZI
  • 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
  • 3D motif for 4YZI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yzi] [4yzi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4YZI: [Bac_rhodopsin ] by SMART
    • Other resources with information on 4YZI
  • Community annotation for 4YZI at PDBWiki (http://pdbwiki.org)

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