Histidinol Phosphate Phosphatase(HPP) soaked with selenourea for 10 min

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol monophosphatase277Medicago truncatulaMutation(s): 0 
Gene Names: MTR_3g117220
Find proteins for G7J7Q5 (Medicago truncatula)
Explore G7J7Q5 
Go to UniProtKB:  G7J7Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7J7Q5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.635α = 90
b = 119.635β = 90
c = 92.906γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

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: 2017-03-15
    Changes: Refinement description
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references