1UXO

The crystal structure of the ydeN gene product from B. subtilis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.125 

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This is version 1.4 of the entry. See complete history. 


Literature

Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution.

Janda, I., Devedjiev, Y., Cooper, D., Chruszcz, M., Derewenda, U., Gabrys, A., Minor, W., Joachimiak, A., Derewenda, Z.S.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1101-1107

  • DOI: 10.1107/S0907444904007188
  • Primary Citation of Related Structures:  
    1UXO

  • PubMed Abstract: 

    • High-throughput (HT) protein crystallography is severely impeded by the relatively low success rate of protein crystallization. Proteins whose structures are not solved in the HT pipeline owing to attrition in any phase of the project are referred to as the high-hanging fruit, in contrast to those proteins that yielded good-quality crystals and crystal structures, which are referred to as low-hanging fruit ...

    High-throughput (HT) protein crystallography is severely impeded by the relatively low success rate of protein crystallization. Proteins whose structures are not solved in the HT pipeline owing to attrition in any phase of the project are referred to as the high-hanging fruit, in contrast to those proteins that yielded good-quality crystals and crystal structures, which are referred to as low-hanging fruit. It has previously been shown that proteins that do not crystallize in the wild-type form can have their surfaces engineered by site-directed mutagenesis in order to create patches of low conformational entropy that are conducive to forming intermolecular interactions. The application of this method to selected proteins from the Bacillus subtilis genome which failed to crystallize in the HT mode is now reported. In this paper, the crystal structure of the product of the YdeN gene is reported. Of three prepared double mutants, i.e. E124A/K127A, E167A/E169A and K88A/Q89A, the latter gave high-quality crystals and the crystal structure was solved by SAD at 1.8 angstroms resolution. The protein is a canonical alpha/beta hydrolase, with an active site that is accessible to solvent.

    Organizational Affiliation: 

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative hydrolase YdeNA192Bacillus subtilisMutation(s): 2 
Gene Names: ydeN, BSU05260
EC: 3
UniProt
Find proteins for P96671 (Bacillus subtilis (strain 168))
Explore P96671 
Go to UniProtKB:  P96671
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.128α = 90
b = 53.971β = 90
c = 93.151γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-27
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2019-09-25
    Changes: Data collection, Experimental preparation, Other