Download MendeleyCrystal structure of putative glucosidase lplD from bacillus subtilis.
Ramagopal, U.A., Rajashankar, K.R., Toro, R., Burley, S.K., Almo, S.C.To be published.
3FEF
Crystal structure of putative glucosidase lplD from bacillus subtilis
- PDB DOI: https://doi.org/10.2210/pdb3FEF/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus subtilis
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-11-28 Released: 2008-12-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.243
- R-Value Work: 0.187
- R-Value Observed: 0.190
wwPDB Validation 3D Report Full Report
This is version 1.4 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 glucosidase lplD, ALPHA-GALACTURONIDASE | A, B, C, D | 450 | Bacillus subtilis | Mutation(s): 0 Gene Names: BSU07130, lplD EC: 3.2.1.67 |  |
UniProt | |||||
Find proteins for P39130 (Bacillus subtilis (strain 168)) Explore P39130 Go to UniProtKB: P39130 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P39130 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| MG Query on MG | G [auth A], J [auth B], L [auth C], O [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| 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: 2.20 Å
- R-Value Free: 0.243
- R-Value Work: 0.187
- R-Value Observed: 0.190
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.987 | α = 69.8 |
| b = 84.843 | β = 68.1 |
| c = 86.051 | γ = 64.07 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| HKL-2000 | data reduction |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2008-12-30 Deposition Author(s): Ramagopal, U.A., Rajashankar, K.R., Toro, R., 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: 2008-12-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2013-03-20
Changes: Structure summary - Version 1.3: 2017-11-01
Changes: Refinement description - Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
