5HDS Signaling Protein date Jan 05, 2016
title Femtosecond Structural Dynamics Drives The Transcis Isomeri Photoactive Yellow Protein: 3 Ps Structure
authors K.Pande, J.Tenboer, M.Schmidt
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
Engineered: Yes
 Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Gene: Pyp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 63
R_factor 0.192 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.900 66.900 40.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
ligand 60F enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceFemtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein., Pande K, Hutchison CD, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Srajer V, Henning R, Spence JC, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt M, Science. 2016 May 6;352(6286):725-9. doi: 10.1126/science.aad5081. Epub 2016 May , 5. PMID:27151871
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (5hds.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 5HDS
  • CSU: Contacts of Structural Units for 5HDS
  • Structure Factors (298 Kb)
  • Retrieve 5HDS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HDS from S2C, [Save to disk]
  • Re-refined 5hds structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HDS 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 5HDS
  • 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: [5hds] [5hds_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5HDS: [PAS ] by SMART
    • Other resources with information on 5HDS
  • Community annotation for 5HDS at PDBWiki (http://pdbwiki.org)

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