1T18

Early intermediate IE1 from time-resolved crystallography of the E46Q mutant of PYP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.5 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, 1T1C

  • 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-resolved Laue crystallography allows structural snapshots (as short as 150 ps) of high crystallographic resolution (approximately 1 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photoactive yellow proteinA125Halorhodospira halophilaMutation(s): 1 
Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16113
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download Ideal Coordinates CCD File 
B [auth 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: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • 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
SHELXmodel building
SHELXL-97refinement
LaueViewdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-09-09
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2021-10-27
    Changes: Database references, Derived calculations