Download MendeleyCrystal 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.
3CZ8
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
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 1.6 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative sporulation-specific glycosylase ydhD | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O05495 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | C [auth A] D [auth A] E [auth A] F [auth A] G [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
- R-Value Work: 0.196
- R-Value Observed: 0.198
- 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 Name | Purpose |
|---|---|
| SHELXD | phasing |
| REFMAC | refinement |
| MAR345 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
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 (Full details and data files)
- 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
