1D7E

CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.

van Aalten, D.M., Crielaard, W., Hellingwerf, K.J., Joshua-Tor, L.

(2000) Protein Sci 9: 64-72

  • DOI: 10.1110/ps.9.1.64
  • Primary Citation of Related Structures:  
    1D7E

  • PubMed Abstract: 

    • The conformational changes during the photocycle of the photoactive yellow protein have been the subject of many recent studies. Spectroscopic measurements have shown that the photocycle also occurs in a crystalline environment, and this has been the basis for subsequent Laue diffraction and cryocrystallographic studies ...

    The conformational changes during the photocycle of the photoactive yellow protein have been the subject of many recent studies. Spectroscopic measurements have shown that the photocycle also occurs in a crystalline environment, and this has been the basis for subsequent Laue diffraction and cryocrystallographic studies. These studies have shown that conformational changes during the photocycle are limited to the chromophore and its immediate environment. However, spectroscopic studies suggest the presence of large conformational changes in the protein. Here, we address this apparent discrepancy in two ways. First, we obtain a description of large concerted motions in the ground state of the yellow protein from NMR data and theoretical calculations. Second, we describe the high-resolution structure of the yellow protein crystallized in a different space group. The structure of the yellow protein differs significantly between the two crystal forms. We show that these differences can be used to obtain a description of the flexibility of the protein that is consistent with the motions observed in solution.

    Related Citations: 
    • 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
      Borgstahl, G.O., Williams, D.R., Getzoff, E.D.
      (1995) Biochemistry 34: 6278
    • Solution structure and backbone dynamics of the photoactive yellow protein.
      Dux, P., Rubinstenn, G., Vuister, G.W., Boelens, R., Mulder, F.A.A.
      (1998) Biochemistry 37: 12689
    Organizational Affiliation: 

    W.M. Keck Structural Biology, Cold Spring Harbor Laboratory, New York 11724, USA. dava@davapc1.bioch.dundee.ac.uk



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOACTIVE YELLOW PROTEIN A122Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
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 
A
4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.561α = 90
b = 40.561β = 90
c = 118.089γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation