3CZ8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative sporulation-specific glycosylase ydhDAB319Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: ydhDBSU05710
EC: 3.2
Find proteins for O05495 (Bacillus subtilis (strain 168))
Explore O05495 
Go to UniProtKB:  O05495
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.965α = 90
b = 84.965β = 90
c = 188.041γ = 120
Software Package:
Software NamePurpose
SHELXDphasing
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-11-14
    Changes: Data collection, Structure summary