1UXO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative hydrolase YdeN
A
192Bacillus subtilis (strain 168)Mutation(s): 2 
Gene Names: ydeN
EC: 3.-.-.-
Find proteins for P96671 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P96671
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 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 = 90.00
b = 53.971β = 90.00
c = 93.151γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SHELXDphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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