1S4R

Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.242 

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:  1S4S

  • 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.


    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: 0.259 
  • R-Value Work: 0.242 
  • 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 reduction
LaueViewdata scaling
SVD4TXdata scaling
KB_SCANdata collection
SVD4TXdata reduction
KB_SCANdata reduction
XTALVIEWrefinement
CNSrefinement

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