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- PDB-3o6d: Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o6d | ||||||
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Title | Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate | ||||||
![]() | Pyridoxine 5'-phosphate synthase | ||||||
![]() | TRANSFERASE / structural genomics / IDP90671 / Center for Structural Genomics of Infectious Diseases / CSGID / pyridoxine synthesis / Vitamin B6 / pyridoxal phosphate / PdxJ / PYRIDOXINE-5'-PHOSPHATE | ||||||
Function / homology | ![]() pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: X-ray crystal structure of pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni. Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.1 KB | Display | ![]() |
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Full document | ![]() | 451.6 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29468.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 11168 / Gene: Cj1238, pdxJ / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: Q9PN59, pyridoxine 5'-phosphate synthase | ||
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#2: Chemical | ChemComp-PXP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.056 M sodium phosphate, 1.344 di-potassium phosphate, (10 mM PYRIDOXINE-5'-PHOSPHATE was used for crystal soaking), pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→31.9 Å / Num. all: 23944 / Num. obs: 23944 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.615 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.98 Å2 / Biso mean: 38.428 Å2 / Biso min: 13.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.949→1.999 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.7432 Å / Origin y: 40.5777 Å / Origin z: 17.3212 Å
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