3CZ8

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

Structural Biology Knowledgebase: 3CZ8 SBKB.org


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 3CZ8

Classification: HYDROLASE

Total Structure Weight: 72852.21

Macromolecule Entities
Molecule Chains Length Organism Details
Putative sporulation-specific glycosylase ydhD A, B 319 Bacillus subtilis EC#: 3.2 IUBMB
Fragment: Residues 96-403
Mutation: D376G
Gene Name(s): ydhD BSU05710
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.96 α = 90.00
b = 84.96 β = 90.00
c = 188.04 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-04-28
  • Released Date: 2008-05-27
  • Deposition author(s): Patskovsky, Y., Romero, R., Rutter, M., Chang, S., Maletic, M., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update