5JD2

SFX structure of corestreptavidin-selenobiotin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.

Hunter, M.S.Yoon, C.H.DeMirci, H.Sierra, R.G.Dao, E.H.Ahmadi, R.Aksit, F.Aquila, A.L.Ciftci, H.Guillet, S.Hayes, M.J.Lane, T.J.Liang, M.Lundstrom, U.Koglin, J.E.Mgbam, P.Rao, Y.Zhang, L.Wakatsuki, S.Holton, J.M.Boutet, S.

(2016) Nat Commun 7: 13388-13388

  • DOI: 10.1038/ncomms13388

  • PubMed Abstract: 
  • Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determinat ...

    Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.


    Organizational Affiliation

    Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B, C, D
120Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BYY
Query on BYY

Download SDF File 
Download CCD File 
A, B, C, D
5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid
selenobiotin
C10 H16 N2 O3 Se
HVUDXAKXEONARI-ZKWXMUAHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.840α = 90.00
b = 98.520β = 112.38
c = 53.430γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata scaling
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United States--

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Advisory, Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-02-14
    Type: Data collection