Download MendeleyThe crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008
Tan, K., Chhor, G., Endres, M., Joachimiak, A.To be published.
4LJS
The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008
- PDB DOI: https://doi.org/10.2210/pdb4LJS/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Veillonella parvula DSM 2008
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-07-05 Released: 2013-07-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.208
- R-Value Work: 0.154
- R-Value Observed: 0.156
wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| Periplasmic binding protein | 324 | Veillonella parvula DSM 2008 | Mutation(s): 0 Gene Names: Vpar_0062 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | C [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | B [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.208
- R-Value Work: 0.154
- R-Value Observed: 0.156
- Space Group: P 62
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 82.994 | α = 90 |
| b = 82.994 | β = 90 |
| c = 110.419 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| ARP | model building |
| WARP | model building |
| HKL-3000 | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
Entry History
Deposition Data
- Released Date: 2013-07-24 Deposition Author(s): Tan, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2013-07-24
Type: Initial release
