1S1Z

Photoactivated chromophore conformation in Photoactive Yellow Protein (E46Q mutant) from 10 to 500 nanoseconds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.060 
  • R-Value Work: 0.051 
  • R-Value Observed: 0.050 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein

Anderson, S.Srajer, V.Pahl, R.Rajagopal, S.Schotte, F.Anfinrud, P.Wulff, M.Moffat, K.

(2004) Structure 12: 1039-1045

  • DOI: 10.1016/j.str.2004.04.008
  • Primary Citation of Related Structures:  
    1S1Z, 1S1Y

  • PubMed Abstract: 
  • We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow prot ...

    We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA. smander@midway.uchicago.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photoactive Yellow ProteinA125Halorhodospira halophilaMutation(s): 1 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download CCD File 
A
4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.060 
  • R-Value Work: 0.051 
  • R-Value Observed: 0.050 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.917α = 90
b = 66.917β = 90
c = 41.002γ = 120
Software Package:
Software NamePurpose
LaueViewdata scaling
LaueViewdata reduction
XTALVIEWrefinement
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description