5T3F

hen egg-white lysozyme soaked with selenourea for 10 min

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

  • Deposited: 2016-08-25 Released: 2016-11-30 
  • Deposition Author(s): Luo, Z., Dauter, Z.
  • Funding Organization(s): National Institutes of Health 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures.

Luo, Z.

(2016) Sci Rep 6: 37123-37123

  • DOI: 10.1038/srep37123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, sel ...

    Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding the crystalline powder of selenourea into mother liquor or cryo-solution with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as donors. Selenourea has different chemical properties than heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules.


    Organizational Affiliation

    Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SEY
Query on SEY

Download SDF File 
Download CCD File 
A
selenourea
C H4 N2 Se
IYKVLICPFCEZOF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.134 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.370α = 90.00
b = 77.370β = 90.00
c = 37.306γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SHELXDphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-25 
  • Released Date: 2016-11-30 
  • Deposition Author(s): Luo, Z., Dauter, Z.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence