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Yorodumi- PDB-2jae: The structure of L-amino acid oxidase from Rhodococcus opacus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jae | ||||||
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Title | The structure of L-amino acid oxidase from Rhodococcus opacus in the unbound state | ||||||
Components | L-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / DIMERISATION MODE / L-AMINO ACID OXIDASE / HYDRIDE TRANSFER MECHANISM / GR2-FAMILY / FLAVOENZYME / FAD CONTAINING | ||||||
Function / homology | Function and homology information L-glutamate oxidase activity / L-phenylalaine oxidase activity / L-lysine oxidase activity / L-amino-acid oxidase / amino acid catabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | RHODOCOCCUS OPACUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Faust, A. / Niefind, K. / Hummel, W. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Structure of a Bacterial L-Amino Acid Oxidase from Rhodococcus Opacus Gives New Evidence for the Hydride Mechanism for Dehydrogenation. Authors: Faust, A. / Niefind, K. / Hummel, W. / Schomburg, D. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and Preliminary X-Ray Analysis of a Bacterial L-Amino-Acid Oxidase from Rhodococcus Opacus Authors: Faust, A. / Geueke, B. / Niefind, K. / Hummel, W. / Schomburg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jae.cif.gz | 399.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jae.ent.gz | 326.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jae_validation.pdf.gz | 895.8 KB | Display | wwPDB validaton report |
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Full document | 2jae_full_validation.pdf.gz | 906.2 KB | Display | |
Data in XML | 2jae_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 2jae_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jae ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jae | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53411.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 46-534 / Source method: isolated from a natural source / Details: DSM 43250 / Source: (natural) RHODOCOCCUS OPACUS (bacteria) / References: UniProt: Q8VPD4, L-amino-acid oxidase #2: Chemical | #3: 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: 2.03 Å3/Da / Density % sol: 39 % |
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Crystal grow | pH: 7.8 / Details: 100MM HEPES PH 7.8 10% 2-PROPANOL 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.816 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.816 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 290588 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.21→1.22 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.9 / % possible all: 92.5 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.25→15.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.032 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→15.98 Å
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