5T3F

hen egg-white lysozyme soaked with selenourea for 10 min

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/srep37123
  • Primary Citation of Related Structures:  
    5T3F, 5T3G, 5T3H, 5T3I, 5T3J, 5T3L

  • 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, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH 2 ) 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SEY
Query on SEY

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
selenourea
C H4 N2 Se
IYKVLICPFCEZOF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.37α = 90
b = 77.37β = 90
c = 37.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary