5T3H

bovine trypsin soaked with selenourea for 5 min


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SEY
Query on SEY

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A
selenourea
C H4 N2 Se
IYKVLICPFCEZOF-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

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Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.878α = 90.00
b = 56.640β = 90.00
c = 65.378γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release