4H35

Feruloyl Esterase Domain of XYNY from Clostridium thermocellum before exposure to 266nm UV laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

In-house UV radiation-damage-induced phasing of selenomethionine-labeled protein structures.

Pereira, P.J.Royant, A.Panjikar, S.de Sanctis, D.

(2013) J.Struct.Biol. 181: 89-94

  • DOI: 10.1016/j.jsb.2012.11.003
  • Primary Citation of Related Structures:  4BAG, 4BAI, 4BAJ

  • PubMed Abstract: 
  • Selenomethionine labeling is the most common technique used in protein crystallography to derivatize recombinant proteins for experimental phasing using anomalous scattering at tunable synchrotron beamlines. Recently, it has been shown that UV radiat ...

    Selenomethionine labeling is the most common technique used in protein crystallography to derivatize recombinant proteins for experimental phasing using anomalous scattering at tunable synchrotron beamlines. Recently, it has been shown that UV radiation depletes electron density of selenium atoms of selenomethionine residues and that UV radiation-damage-induced phasing (equivalent to single isomorphous replacement) protocol can be applied to calculate experimental phases. Here we present the straightforward integration of a UV source with an in-house diffractometer. We show how this setup can extend the capabilities of a sealed tube X-ray generator and be used for experimental phasing of selenium-labeled proteins.


    Organizational Affiliation

    IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase Y
A, B
297Clostridium thermocellumGene Names: xynY
EC: 3.2.1.8
Find proteins for P51584 (Clostridium thermocellum)
Go to UniProtKB:  P51584
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.370α = 90.00
b = 108.400β = 90.00
c = 112.860γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
XSCALEdata scaling
CrysalisProdata collection
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description