4BBU Signaling Protein date Sep 27, 2012
title The Pr2 Photocycle Intermediate Of Photoactive Yellow Protei
authors F.Schotte, H.S.Cho, V.R.I.Kaila, H.Kamikubo, N.Dashdorj, E.R.Henr T.J.Graber, R.Henning, M.Wulff, G.Hummer, M.Kataoka, P.A.Anfinru
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
Engineered: Yes
 Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 63
R_factor 0.165 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.833 66.833 40.947 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
ligand HC4 enzyme
note 4BBU (Molecule of the Month:pdb183)
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceWatching a signaling protein function in real time via 100-ps time-resolved Laue crystallography., Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA, Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19256-61. doi:, 10.1073/pnas.1210938109. Epub 2012 Nov 6. PMID:23132943
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (4bbu.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 4BBU
  • CSU: Contacts of Structural Units for 4BBU
  • Structure Factors (78 Kb)
  • Retrieve 4BBU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BBU from S2C, [Save to disk]
  • Re-refined 4bbu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4BBU 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 4BBU
  • 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 4BBU, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bbu] [4bbu_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BBU: [PAS ] by SMART
    • Other resources with information on 4BBU
  • Community annotation for 4BBU at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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