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1s4r
From Proteopedia
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|PDB= 1s4r |SIZE=350|CAPTION= <scene name='initialview01'>1s4r</scene>, resolution 1.9Å | |PDB= 1s4r |SIZE=350|CAPTION= <scene name='initialview01'>1s4r</scene>, resolution 1.9Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=HC4:4 | + | |LIGAND= <scene name='pdbligand=HC4:4'-HYDROXYCINNAMIC ACID'>HC4</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
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[[Category: reaction intermediate]] | [[Category: reaction intermediate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:34:08 2008'' |
Revision as of 11:34, 23 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis
Overview
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.
About this Structure
1S4R is a Single protein structure of sequence from Halorhodospira halophila. Full crystallographic information is available from OCA.
Reference
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, Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4799-804. Epub 2004 Mar 23. PMID:15041745
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