Download MendeleyX-ray crystal structure of pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni.
Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.To be published.
3O6D
Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate
- PDB DOI: https://doi.org/10.2210/pdb3O6D/pdb
- Classification: TRANSFERASE
- Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-07-28 Released: 2010-08-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.197
- R-Value Work: 0.170
- R-Value Observed: 0.171
This is version 1.3 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 |
| Pyridoxine 5'-phosphate synthase | 260 | Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 | Mutation(s): 0 Gene Names: Cj1238, pdxJ EC: 2.6.99.2 |  | |
UniProt | |||||
Find proteins for Q9PN59 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PN59 Go to UniProtKB: Q9PN59 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9PN59 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PXP Query on PXP | B [auth A] | PYRIDOXINE-5'-PHOSPHATE C8 H12 N O6 P WHOMFKWHIQZTHY-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | C [auth A], D [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| 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: 1.95 Å
- R-Value Free: 0.197
- R-Value Work: 0.170
- R-Value Observed: 0.171
- Space Group: I 4 2 2
- Diffraction Data: https://doi.org/10.18430/m33o6d
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.239 | α = 90 |
| b = 90.239 | β = 90 |
| c = 156.081 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | phasing |
| SOLVE | phasing |
| RESOLVE | phasing |
| HKL-3000 | phasing |
Entry History
Deposition Data
- Released Date: 2010-08-11 Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2010-08-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary
