4WL9

Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

Tenboer, J.Basu, S.Zatsepin, N.Pande, K.Milathianaki, D.Frank, M.Hunter, M.Boutet, S.Williams, G.J.Koglin, J.E.Oberthuer, D.Heymann, M.Kupitz, C.Conrad, C.Coe, J.Roy-Chowdhury, S.Weierstall, U.James, D.Wang, D.Grant, T.Barty, A.Yefanov, O.Scales, J.Gati, C.Seuring, C.Srajer, V.Henning, R.Schwander, P.Fromme, R.Ourmazd, A.Moffat, K.Van Thor, J.J.Spence, J.C.Fromme, P.Chapman, H.N.Schmidt, M.

(2014) Science 346: 1242-1246

  • DOI: 10.1126/science.1259357
  • Primary Citation of Related Structures:  
    4WL9, 4WLA

  • PubMed Abstract: 
  • Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1 ...

    Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.


    Organizational Affiliation

    Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA. m-schmidt@uwm.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photoactive yellow proteinA125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16113
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download Ideal Coordinates CCD File 
B [auth A]4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.9α = 90
b = 66.9β = 90
c = 40.8γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations