Download MendeleyCrystal Structure of Periplasmic Binding Protein type 1 from Bordetella pertussis Tohama I complexed with 3-Hydroxy Benzoic Acid
Kim, Y., Joachimiak, G., Clancy, S., Joachimiak, A.To be published.
4Q6W | pdb_00004q6w
Crystal Structure of Periplasmic Binding Protein type 1 from Bordetella pertussis Tohama I complexed with 3-Hydroxy Benzoic Acid
- PDB DOI: https://doi.org/10.2210/pdb4Q6W/pdb
- Classification: Structural Genomics, Unknown Function
- Organism(s): Bordetella pertussis Tohama I
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-04-23 Released: 2014-07-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.204 (Depositor), 0.204 (DCC)
- R-Value Work: 0.175 (Depositor), 0.176 (DCC)
- R-Value Observed: 0.177 (Depositor)
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 |
| Putative leu/ile/val-binding protein | 403 | Bordetella pertussis Tohama I | Mutation(s): 0 Gene Names: BP0622 |  | |
UniProt | |||||
Find proteins for Q7VS30 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VS30 Go to UniProtKB: Q7VS30 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7VS30 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 3HB Query on 3HB | C [auth A], I [auth B] | 3-HYDROXYBENZOIC ACID C7 H6 O3 IJFXRHURBJZNAO-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | J [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], F [auth A], G [auth A], K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| 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: 1.84 Å
- R-Value Free: 0.204 (Depositor), 0.204 (DCC)
- R-Value Work: 0.175 (Depositor), 0.176 (DCC)
- R-Value Observed: 0.177 (Depositor)
Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 112.638 | α = 90 |
| b = 138.041 | β = 90 |
| c = 57.251 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| RESOLVE | model building |
| Coot | model building |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
| RESOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2014-07-02 Deposition Author(s): Kim, Y., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-07-02
Type: Initial release - Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
