1TS6

Structure of the pB2 intermediate from time-resolved Laue crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.

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

(2005) Proc.Natl.Acad.Sci.Usa 102: 7145-7150

  • DOI: 10.1073/pnas.0409035102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermed ...

    Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.


    Organizational Affiliation

    Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. hyotcherl.ihee@kaist.ac.kr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoactive yellow protein
A
125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.175 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.833α = 90.00
b = 66.833β = 90.00
c = 40.947γ = 120.00
Software Package:
Software NamePurpose
LaueViewdata reduction
SHELXL-97refinement
LAUEVIEWdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-09-09
    Type: Other