Download MendeleyCrystal structure of Pyridoxamine kinase PDXY from Burkholderia xenovorans
Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edewards, T.E.To be published.
5TRW
Crystal structure of Pyridoxamine kinase PDXY from Burkholderia xenovorans
- PDB DOI: https://doi.org/10.2210/pdb5TRW/pdb
- Classification: TRANSFERASE
- Organism(s): Paraburkholderia xenovorans LB400
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-10-27 Released: 2016-11-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.179
- R-Value Work: 0.151
- R-Value Observed: 0.152
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Pyridoxal kinase PdxY | 296 | Paraburkholderia xenovorans LB400 | Mutation(s): 0 Gene Names: pdxY, Bxeno_A1503, Bxe_A2936 EC: 2.7.1.35 |  | |
UniProt | |||||
Find proteins for Q141E8 (Paraburkholderia xenovorans (strain LB400)) Explore Q141E8 Go to UniProtKB: Q141E8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q141E8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NHE Query on NHE | D [auth A] | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | E [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | H [auth A], I [auth A], J [auth A], K [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| NO3 Query on NO3 | B [auth A], C [auth A] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A], G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.179
- R-Value Work: 0.151
- R-Value Observed: 0.152
- Space Group: P 41 21 2
- Diffraction Data: https://doi.org/10.18430/M35TRW
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.87 | α = 90 |
| b = 58.87 | β = 90 |
| c = 175.77 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| BALBES | phasing |
| Coot | model building |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2016-11-09 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-11-09
Type: Initial release - Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description - Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
