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- PDB-6ylz: X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ylz | ||||||
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Title | X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli | ||||||
![]() | Pyridoxine/pyridoxamine 5'-phosphate oxidase | ||||||
![]() | FLAVOPROTEIN / Pyridoxal 5'-phosphate / Vitamine B6 metabolism / oxidase | ||||||
Function / homology | ![]() 'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity ...'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Battista, T. / Sularea, M. / Barile, A. / Fiorillo, A. / Tramonti, A. / Ilari, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase. Authors: Barile, A. / Battista, T. / Fiorillo, A. / di Salvo, M.L. / Malatesta, F. / Tramonti, A. / Ilari, A. / Contestabile, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 795.9 KB | Display | ![]() |
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Full document | ![]() | 794.8 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ymhC ![]() 1g76S S: Starting model for refinement C: citing same article ( |
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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: 25442.062 Da / Num. of mol.: 1 / Mutation: K72I, Y129F, R133L, H199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: pdxH, b1638, JW1630 / Production host: ![]() ![]() References: UniProt: P0AFI7, UniProt: E2QMK2*PLUS, pyridoxal 5'-phosphate synthase | ||||||
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#2: Chemical | ChemComp-FMN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM KPHO pH 7,5, 5 mM 2-mercaptoethanol, 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.558→55.233 Å / Num. obs: 41877 / % possible obs: 98 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03 / Rrim(I) all: 0.134 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.558→1.585 Å / Redundancy: 11.91 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2040 / CC1/2: 0.444 / Rpim(I) all: 0.803 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G76 Resolution: 1.558→55.232 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.865 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.074 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.558→55.232 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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