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 

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

  • 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 ...

    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: 
    • 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
    • 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

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
A
122Halorhodospira halophilaMutation(s): 0 
Gene 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: 1.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.139 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 40.561α = 90.00
b = 40.561β = 90.00
c = 118.089γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
SHELXL-97refinement
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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