1KOU

Crystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.

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

(2002) Acta Crystallogr.,Sect.D 58: 585-590


  • PubMed Abstract: 
  • A structural study is described of the photoactive yellow protein (PYP) reconstituted with the chromophore derivative 3,4-dihydroxycinnamic acid. The crystal structure of PYP reconstituted with this chromophore at 1.16 A resolution is reported in spa ...

    A structural study is described of the photoactive yellow protein (PYP) reconstituted with the chromophore derivative 3,4-dihydroxycinnamic acid. The crystal structure of PYP reconstituted with this chromophore at 1.16 A resolution is reported in space group P6(5). This is the first high-resolution structure of a photoreceptor containing a modified chromophore. The introduction of an extra hydroxyl group in the native chromophore (i.e. p-coumaric acid) appears to perturb the structure of the hybrid yellow protein only slightly. The chromophore is bound by the protein in two different conformations, separated by a rotation of 180 degrees of the catechol ring. In combination with available spectroscopic data, it is concluded that the caffeic acid chromophore binds to the protein in a strained conformation, which leads to a faster ejection from the chromophore-binding pocket upon pB formation.


    Organizational Affiliation

    W. M. Keck Structural Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
A
125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHC
Query on DHC

Download SDF File 
Download CCD File 
A
CAFFEIC ACID
3,4-DIHYDROXYCINNAMIC ACID
C9 H8 O4
QAIPRVGONGVQAS-DUXPYHPUSA-N
 Ligand Interaction
NBU
Query on NBU

Download SDF File 
Download CCD File 
A
N-BUTANE
C4 H10
IJDNQMDRQITEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 40.582α = 90.00
b = 40.582β = 90.00
c = 117.801γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    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: 2017-10-11
    Type: Advisory, Refinement description