1T1C

Late intermediate IL3 from time-resolved crystallography of the E46Q mutant of PYP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A Structural Pathway for Signaling in the E46Q Mutant of Photoactive Yellow Protein

Rajagopal, S.Anderson, S.Srajer, V.Schmidt, M.Pahl, R.Moffat, K.

(2005) Structure 13: 55-63

  • DOI: 10.1016/j.str.2004.10.016
  • Primary Citation of Related Structures:  1T18, 1T19, 1T1A, 1T1B

  • PubMed Abstract: 
  • In the bacterial photoreceptor photoactive yellow protein (PYP), absorption of blue light by its chromophore leads to a conformational change in the protein associated with differential signaling activity, as it executes a reversible photocycle. Time ...

    In the bacterial photoreceptor photoactive yellow protein (PYP), absorption of blue light by its chromophore leads to a conformational change in the protein associated with differential signaling activity, as it executes a reversible photocycle. Time-resolved Laue crystallography allows structural snapshots (as short as 150 ps) of high crystallographic resolution (approximately 1.6 A) to be taken of a protein as it functions. Here, we analyze by singular value decomposition a comprehensive time-resolved crystallographic data set of the E46Q mutant of PYP throughout the photocycle spanning 10 ns-100 ms. We identify and refine the structures of five distinct intermediates and provide a plausible chemical kinetic mechanism for their inter conversion. A clear structural progression is visible in these intermediates, in which a signal generated at the chromophore propagates through a distinct structural pathway of conserved residues and results in structural changes near the N terminus, over 20 A distant from the chromophore.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoactive yellow protein
A
125Halorhodospira halophilaGene 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: 0.139 
  • R-Value Work: 0.129 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.917α = 90.00
b = 66.917β = 90.00
c = 41.002γ = 120.00
Software Package:
Software NamePurpose
LaueViewdata scaling
SHELXmodel building
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    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
  • Version 1.4: 2017-10-11
    Type: Refinement description