Download MendeleyCrystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine
Bonanno, J.B., Rutter, M., Bain, K.T., Miller, S., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C.To be published.
3I6V
Crystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine
- PDB DOI: https://doi.org/10.2210/pdb3I6V/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Ruegeria pomeroyi
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-07-07 Released: 2009-07-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.224
- R-Value Work: 0.198
- R-Value Observed: 0.200
wwPDB Validation 3D Report Full Report
This is version 1.5 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 His/Glu/Gln/Arg/opine family-binding protein | 232 | Ruegeria pomeroyi | Mutation(s): 0 Gene Names: SPO1306 |  | |
UniProt | |||||
Find proteins for Q5LTV6 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LTV6 Go to UniProtKB: Q5LTV6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LTV6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| LYS Query on LYS | B [auth A] | LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.224
- R-Value Work: 0.198
- R-Value Observed: 0.200
- Space Group: P 43 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.931 | α = 90 |
| b = 70.931 | β = 90 |
| c = 141.359 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| SHELXCD | phasing |
| SHELXE | model building |
Entry History
Deposition Data
- Released Date: 2009-07-21 Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Miller, S., Romero, R., Sauder, J.M., 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: 2009-07-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2018-11-21
Changes: Data collection, Structure summary - Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.5: 2024-02-21
Changes: Data collection, Database references
