Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.05 kDa 
• Atom Count: 1135 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

2PYP

PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, 50% BLEACHED

• DOI: 10.2210/pdb2PYP/pdb

• Classification: PHOTORECEPTOR
• Organism(s): Halorhodospira halophila
• Mutation(s): No 


• Deposited: 1997-02-03 Released: 1998-04-29 
• Deposition Author(s): Genick, U.K., Borgstahl, G.E.O., Ng, K., Ren, Z., Pradervand, C., Burke, P., Srajer, V., Teng, T., Schildkamp, W., Mcree, D.E., Moffat, K., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Structure of a protein photocycle intermediate by millisecond time-resolved crystallography.

Genick, U.K., Borgstahl, G.E., Ng, K., Ren, Z., Pradervand, C., Burke, P.M., Srajer, V., Teng, T.Y., Schildkamp, W., McRee, D.E., Moffat, K., Getzoff, E.D.

(1997) Science 275: 1471-1475

• PubMed: 9045611 
• DOI: 10.1126/science.275.5305.1471
• Primary Citation of Related Structures:  
  2PYP


• PubMed Abstract: 
  

The blue-light photoreceptor photoactive yellow protein (PYP) undergoes a self-contained light cycle. The atomic structure of the bleached signaling intermediate in the light cycle of PYP was determined by millisecond time-resolved, multiwavelength Laue crystallography and simultaneous optical spectroscopy. Light-induced trans-to-cis isomerization of the 4-hydroxycinnamyl chromophore and coupled protein rearrangements produce a new set of active-site hydrogen bonds. An arginine gateway opens, allowing solvent exposure and protonation of the chromophore's phenolic oxygen. Resulting changes in shape, hydrogen bonding, and electrostatic potential at the protein surface form a likely basis for signal transduction. The structural results suggest a general framework for the interpretation of protein photocycles.

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Organizational Affiliation: 

Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOACTIVE YELLOW PROTEIN	A	125	Halorhodospira halophila	Mutation(s): 0  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: 1.90 Å
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.9	α = 90
b = 66.9	β = 90
c = 40.8	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
LaueView	data reduction
LaueView	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-02-03 
• Released Date: 1998-04-29 
Deposition Author(s): Genick, U.K., Borgstahl, G.E.O., Ng, K., Ren, Z., Pradervand, C., Burke, P., Srajer, V., Teng, T., Schildkamp, W., Mcree, D.E., Moffat, K., Getzoff, E.D.

Revision History  

• Version 1.0: 1998-04-29
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other, Refinement description