5HD3 Signaling Protein date Jan 04, 2016
title Femtosecond Structural Dynamics Drives The Transcis Isomeri Photoactive Yellow Protein: Dark Structure Of Photoactive Y Protein
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 0.154 R_Free 0.181
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] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (5hd3.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 5HD3
  • CSU: Contacts of Structural Units for 5HD3
  • Structure Factors (334 Kb)
  • Retrieve 5HD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HD3 from S2C, [Save to disk]
  • Re-refined 5hd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HD3 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 5HD3
  • 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: [5hd3] [5hd3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5HD3: [PAS ] by SMART
    • Other resources with information on 5HD3
  • Community annotation for 5HD3 at PDBWiki (http://pdbwiki.org)

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