1S4S

Reaction Intermediate in the Photocycle of PYP, intermediate occupied between 100 micro-seconds to 5 milli-seconds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data

Schmidt, M.Pahl, R.Srajer, V.Anderson, S.Ren, Z.Ihee, H.Rajagopal, S.Moffat, K.

(2004) Proc.Natl.Acad.Sci.USA 101: 4799-4804

  • DOI: 10.1073/pnas.0305983101
  • Primary Citation of Related Structures:  1S4R

  • PubMed Abstract: 
  • We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of ...

    We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.


    Related Citations: 
    • Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data
      Schmidt, M.,Rajagopal, S.,Ren, Z.,Moffat, K.
      (2003) Biophys.J. 84: 2112


    Organizational Affiliation

    Physikdepartment E17, Technische Universit√§t M√ľnchen, 85747 Garching, Germany. marius@hexa.e17.physik.tu-muenchen.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoactive yellow protein
A
125Halorhodospira halophilaGene 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: 1.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.900α = 90.00
b = 66.900β = 90.00
c = 40.800γ = 120.00
Software Package:
Software NamePurpose
LaueViewdata scaling
KB_SCANdata reduction
SVD4TXdata scaling
XTALVIEWrefinement
CNSrefinement
LaueViewdata reduction
SVD4TXdata reduction
KB_SCANdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description