3CZ8 | pdb_00003cz8

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

• PDB DOI: https://doi.org/10.2210/pdb3CZ8/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-04-28 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.85 kDa 
• Atom Count: 5,148 
• Modeled Residue Count: 600 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sporulation-specific glycosylase ydhD	A, B	319	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1  Gene Names: ydhD, BSU05710 EC: 3.2
UniProt
Find proteins for O05495 (Bacillus subtilis (strain 168)) Explore O05495  Go to UniProtKB:  O05495

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.965	α = 90
b = 84.965	β = 90
c = 188.041	γ = 120

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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  

• 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
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.6: 2024-02-21
  Changes: Data collection, Refinement description