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Yorodumi- PDB-3ayj: X-ray crystal structures of L-phenylalanine oxidase (deaminating ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ayj | ||||||
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Title | X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism | ||||||
Components | Pro-enzyme of L-phenylalanine oxidase | ||||||
Keywords | OXIDOREDUCTASE / L-PHENYLALANINE OXIDASE / AMINO ACID OXIDASE / FLAVOENZYME / L-Phe Binding | ||||||
Function / homology | Function and homology information phenylalanine 2-monooxygenase / phenylalanine 2-monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Ida, K. / Suguro, M. / Suzuki, H. | ||||||
Citation | Journal: J.Biochem. / Year: 2011 Title: High resolution X-ray crystal structures of L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism Authors: Ida, K. / Suguro, 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 | 3ayj.cif.gz | 633.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ayj.ent.gz | 515.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ayj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/3ayj ftp://data.pdbj.org/pub/pdb/validation_reports/ay/3ayj | HTTPS FTP |
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-Related structure data
Related structure data | 3ayiC 3aylC 2yr4S C: citing same article (ref.) S: Starting model for refinement |
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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
-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.) Pseudomonas (bacteria) / Strain: P-501 / Gene: propao / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5W9R9, phenylalanine 2-monooxygenase |
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-Non-polymers , 5 types, 2345 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES PH7.5, 1.0M AMMONIUM SULFATE, pH 7.50, VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.8 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→29.2 Å / Num. obs: 615937 / % possible obs: 98.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.398 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YR4 Resolution: 1.1→29.2 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.592 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R Free: 0.022 / 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: 11.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.13 Å / Total num. of bins used: 20
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