1S1Y | pdb_00001s1y

Photoactivated chromophore conformation in Photoactive Yellow Protein (E46Q mutant) from 10 microseconds to 3 milliseconds

• PDB DOI: https://doi.org/10.2210/pdb1S1Y/pdb

• Classification: PHOTORECEPTOR
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-01-07 Released: 2004-06-15 
• Deposition Author(s): Anderson, S., Srajer, V., Pahl, R., Rajagopal, S., Schotte, F., Anfinrud, P., Wulff, M., Moffat, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.070 (Depositor) 
• R-Value Work: 
  0.064 (Depositor) 
• R-Value Observed: 
  0.066 (Depositor) 

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

• PubMed: 15274923 
• DOI: https://doi.org/10.1016/j.str.2004.04.008
• Primary Citation Related Structures: 
  1S1Y, 1S1Z


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.05 kDa 
• Atom Count: 1,355 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 1  Gene Names: PYP
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113  Go to UniProtKB:  P16113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC4	B [auth A]	4'-HYDROXYCINNAMIC ACID C9 H8 O3 NGSWKAQJJWESNS-ZZXKWVIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.070 (Depositor) 
• R-Value Work:  0.064 (Depositor) 
• R-Value Observed: 0.066 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.917	α = 90
b = 66.917	β = 90
c = 41.002	γ = 120

Software Package:

Software Name	Purpose
LaueView	data scaling
LaueView	data reduction
XTALVIEW	refinement
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Anderson, S., Srajer, V., Pahl, R., Rajagopal, S., Schotte, F., Anfinrud, P., Wulff, M., Moffat, K.

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
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations