Download MendeleyCrystal structure of a DinB-like Protein (NP_389123.1) from BACILLUS SUBTILIS at 2.30 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3DKA
Crystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3DKA/pdb
- Classification: UNKNOWN FUNCTION
- Organism(s): Bacillus subtilis
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-06-24 Released: 2008-08-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.269
- R-Value Work: 0.217
- R-Value Observed: 0.219
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 |
| DinB-like Protein | 155 | Bacillus subtilis | Mutation(s): 0 Gene Names: NP_389123.1, yjoA, BSU12410 |  | |
UniProt | |||||
Find proteins for O34334 (Bacillus subtilis (strain 168)) Explore O34334 Go to UniProtKB: O34334 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O34334 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.269
- R-Value Work: 0.217
- R-Value Observed: 0.219
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M33DKA
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.69 | α = 90 |
| b = 63.34 | β = 90 |
| c = 82.06 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-08-19 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-08-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references
