Download MendeleyStructure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
Campopiano, D.J., Serpico, A., Marles-Wright, J.To be published.
6HBV | pdb_00006hbv
Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
- PDB DOI: https://doi.org/10.2210/pdb6HBV/pdb
- Classification: TRANSFERASE
- Organism(s): Sphingopyxis macrogoltabida
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-08-13 Released: 2019-08-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.174 (Depositor), 0.180 (DCC)
- R-Value Work: 0.143 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.144 (Depositor)
Starting Model: experimental
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This is version 1.2 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 |
| Aminopentol aminotransferase | 440 | Sphingopyxis macrogoltabida | Mutation(s): 0 Gene Names: fumI EC: 2.6.1 |  | |
UniProt | |||||
Find proteins for D2D3B2 (Sphingopyxis macrogoltabida) Explore D2D3B2 Go to UniProtKB: D2D3B2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D2D3B2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PMP Query on PMP | D [auth A], G [auth B] | 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N |  | ||
| PLP Query on PLP | C [auth A], F [auth B] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.174 (Depositor), 0.180 (DCC)
- R-Value Work: 0.143 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.144 (Depositor)
Diffraction Data: https://doi.org/10.5281/zenodo.1344451
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.254 | α = 90 |
| b = 103.903 | β = 109.61 |
| c = 65.326 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2019-08-28 Deposition Author(s): Campopiano, D.J., Serpico, A., Marles-Wright, J.
Revision History (Full details and data files)
- Version 1.0: 2019-08-28
Type: Initial release - Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-08-07
Changes: Database references
