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Open data
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Basic information
Entry | Database: PDB / ID: 8qyw | ||||||
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Title | Human Pyridoxine-5'-phosphate oxidase mutant R225H | ||||||
![]() | Pyridoxine-5'-phosphate oxidase | ||||||
![]() | OXIDOREDUCTASE / Pyridoxine biosynthesis / Flavoprotein / Pyridoxal phosphate | ||||||
Function / homology | ![]() pyridoxamine metabolic process / pyridoxal 5'-phosphate synthase / Vitamin B6 activation to pyridoxal phosphate / pyridoxamine phosphate oxidase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / pyridoxal phosphate binding / FMN binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antonelli, L. / Ilari, A. / Fiorillo, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Identification of the pyridoxal 5'-phosphate allosteric site in human pyridox(am)ine 5'-phosphate oxidase. Authors: Barile, A. / Graziani, C. / Antonelli, L. / Parroni, A. / Fiorillo, A. / di Salvo, M.L. / Ilari, A. / Giorgi, A. / Rosignoli, S. / Paiardini, A. / Contestabile, R. / Tramonti, 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 | ![]() | 60.3 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.4 KB | Display | ![]() |
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Full document | ![]() | 765.9 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qytC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30292.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and ...Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and therefore we were not able to reconstruct these segments. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NVS9, pyridoxal 5'-phosphate synthase | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-FMN / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1 M Ammonium Sulfate, 2% PEG400, 0.1 M HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.746→71.78 Å / Num. obs: 6519 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.999 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.747→2.792 Å / Num. unique obs: 323 / CC1/2: 0.866 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.813 Å2
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Refinement step | Cycle: 1 / Resolution: 2.746→41.47 Å
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