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Yorodumi- PDB-2yr4: Crystal structure of L-phenylalanine oxiase from Psuedomonas sp. P-501 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yr4 | ||||||
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Title | Crystal structure of L-phenylalanine oxiase from Psuedomonas sp. P-501 | ||||||
Components | Pro-enzyme of L-phenylalanine oxidase | ||||||
Keywords | OXIDOREDUCTASE / L-phenylalanine oxidase / amino oxidase / flavoenzyme | ||||||
Function / homology | Function and homology information phenylalanine 2-monooxygenase / phenylalanine 2-monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. P-501 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Ida, K. / Kurabayashi, M. / Suguro, M. / Suzuki, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural basis of proteolytic activation of L-phenylalanine oxidase from Pseudomonas sp. P-501. Authors: Ida, K. / Kurabayashi, M. / Suguro, M. / Hiruma, Y. / Hikima, T. / Yamomoto, M. / Suzuki, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yr4.cif.gz | 302.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yr4.ent.gz | 239.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yr4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2yr4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2yr4_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 2yr4_validation.cif.gz | 98 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/2yr4 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/2yr4 | HTTPS FTP |
-Related structure data
Related structure data | 2yr5C 2yr6C 2yr7 2yr8 2yr9 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77899.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. P-501 (bacteria) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5W9R9, phenylalanine 2-monooxygenase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1.7M ammonium sulfate, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50.77 Å / Num. obs: 184918 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.272 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→50.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.665 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CNS was also used for the refinement. HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.826 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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