Download MendeleyCrystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021
Agarwal, R., Almo, S.C., Swaminathan, S.To be published.
4E1J
Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021
- PDB DOI: https://doi.org/10.2210/pdb4E1J/pdb
- Classification: TRANSFERASE
- Organism(s): Sinorhizobium meliloti 1021
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2012-03-06 Released: 2012-03-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.33 Å
- R-Value Free: 0.290
- R-Value Work: 0.230
- R-Value Observed: 0.233
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 |
| Glycerol kinase | 520 | Sinorhizobium meliloti 1021 | Mutation(s): 0 Gene Names: glpK, RB1135, SMb21009 EC: 2.7.1.30 |  | |
UniProt | |||||
Find proteins for O86033 (Rhizobium meliloti (strain 1021)) Explore O86033 Go to UniProtKB: O86033 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O86033 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth A], G [auth B], I [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | F [auth A], J [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.33 Å
- R-Value Free: 0.290
- R-Value Work: 0.230
- R-Value Observed: 0.233
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.22 | α = 90 |
| b = 101.975 | β = 90.03 |
| c = 107.548 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| AutoSol | phasing |
| PHENIX | model building |
| Coot | model building |
| CCP4 | model building |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2012-03-21 Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)
Revision History (Full details and data files)
- Version 1.0: 2012-03-21
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description
