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- PDB-2yr6: Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yr6 | |||||||||
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Title | Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501 | |||||||||
![]() | Pro-enzyme of L-phenylalanine oxidase | |||||||||
![]() | OXIDOREDUCTASE / L-phenylalanine oxidase / amino oxidase / flavoenzyme | |||||||||
Function / homology | ![]() phenylalanine 2-monooxygenase / phenylalanine 2-monooxygenase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ida, K. / Kurabayashi, M. / Suguro, M. / Suzuki, H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 621.6 KB | Display | ![]() |
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PDB format | ![]() | 504.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.2 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 75.3 KB | Display | |
Data in CIF | ![]() | 115.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yr4SC ![]() 2yr5C ![]() 2yr7 ![]() 2yr8 ![]() 2yr9 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 77899.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1965 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/BE2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/BE2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES pH7.5, 1.0M ammonium sulfate, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→34.18 Å / Num. obs: 339311 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.342 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YR4 Resolution: 1.35→34.18 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.122 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 12.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→34.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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