5T3H | pdb_00005t3h

bovine trypsin soaked with selenourea for 5 min

• PDB DOI: https://doi.org/10.2210/pdb5T3H/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

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

Luo, Z.

(2016) Sci Rep 6: 37123-37123

• PubMed: 27841370 
• DOI: https://doi.org/10.1038/srep37123
• Primary Citation 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.

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Organizational Affiliation: 
• Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, 60439, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25 kDa 
• Atom Count: 1,881 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEY	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	selenourea C H4 N2 Se IYKVLICPFCEZOF-UHFFFAOYSA-N
BEN	C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	N [auth A], O [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.878	α = 90
b = 56.64	β = 90
c = 65.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary