3CZ8

Crystal structure of putative sporulation-specific glycosylase ydhD from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of putative glycosylase ydhD from Bacillus subtilis.

Patskovsky, Y.Romero, R.Rutter, M.Chang, S.Maletic, M.Smith, D.Wasserman, S.R.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative sporulation-specific glycosylase ydhD
A, B
319Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: ydhD
EC: 3.2.-.-
Find proteins for O05495 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O05495
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 84.965α = 90.00
b = 84.965β = 90.00
c = 188.041γ = 120.00
Software Package:
Software NamePurpose
SHELXDphasing
HKL-2000data reduction
HKL-2000data scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description