Download MendeleyCrystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus subtilis
Nocek, B., Stein, A., Wu, R., Jedrzejczak, R., Joachimiak, A.To be published.
3GYG
Crystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus subtilis
- PDB DOI: https://doi.org/10.2210/pdb3GYG/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus subtilis subsp. subtilis str. 168
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-04-03 Released: 2009-05-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.277
- R-Value Work: 0.210
- R-Value Observed: 0.214
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| NTD biosynthesis operon putative hydrolase ntdB | 289 | Bacillus subtilis subsp. subtilis str. 168 | Mutation(s): 0 Gene Names: ntdB, yhjK, BSU10540 |  | |
UniProt | |||||
Find proteins for O07565 (Bacillus subtilis (strain 168)) Explore O07565 Go to UniProtKB: O07565 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O07565 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | E [auth A], F [auth B], G [auth C], H [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.277
- R-Value Work: 0.210
- R-Value Observed: 0.214
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.077 | α = 90 |
| b = 111.732 | β = 90 |
| c = 135.173 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | phasing |
| SHELXD | phasing |
| MLPHARE | phasing |
| Coot | model building |
| PHENIX | model building |
| CCP4 | model building |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | phasing |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2009-05-12 Deposition Author(s): Nocek, B., Stein, A., Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-05-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
