Download MendeleyCrystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula
Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
4MO9
Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula
- PDB DOI: https://doi.org/10.2210/pdb4MO9/pdb
- Classification: SOLUTE-BINDING PROTEIN
- Organism(s): Veillonella parvula DSM 2008
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2013-09-11 Released: 2013-09-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.93 Å
- R-Value Free: 0.199
- R-Value Work: 0.166
- R-Value Observed: 0.168
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Periplasmic binding protein | 369 | Veillonella parvula DSM 2008 | Mutation(s): 0 Gene Names: Vpar_0195 |  | |
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 | |
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| TMO Query on TMO | B [auth A] | trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-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: 1.93 Å
- R-Value Free: 0.199
- R-Value Work: 0.166
- R-Value Observed: 0.168
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 39.402 | α = 90 |
| b = 75.999 | β = 90 |
| c = 125.187 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXS | phasing |
| MLPHARE | phasing |
| DM | model building |
| ARP/wARP | model building |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
Entry History
Deposition Data
- Released Date: 2013-09-25 Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2013-09-25
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description
