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Yorodumi- PDB-2jb1: The L-amino acid oxidase from Rhodococcus opacus in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jb1 | ||||||
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Title | The L-amino acid oxidase from Rhodococcus opacus in complex with L- alanine | ||||||
Components | L-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / DIMERISATION MODE / L-AMINO ACID OXIDASE / HYDRIDE TRANSFER MECHANISM / GR2-FAMILY / FLAVOENZYME / REDUCED FAD / FAD CONTAINING | ||||||
Function / homology | Function and homology information L-glutamate oxidase activity / L-phenylalaine oxidase activity / L-lysine oxidase activity / L-amino-acid oxidase / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | RHODOCOCCUS OPACUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 2jb1.cif.gz | 410.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jb1.ent.gz | 335.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jb1 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jb1 | HTTPS FTP |
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-Related structure data
Related structure data | 2jaeSC 2jb2C 2jb3C S: Starting model for refinement 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
#1: Protein | Mass: 53411.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 46-534 / Source method: isolated from a natural source Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM 43250 Source: (natural) RHODOCOCCUS OPACUS (bacteria) / References: UniProt: Q8VPD4, L-amino-acid oxidase #2: Chemical | #3: Chemical | #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: 2.4 Å3/Da / Density % sol: 40 % |
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Crystal grow | pH: 7.8 / Details: 100MM HEPES PH 7.8 10% 2-PROPANOL 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9195 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→15 Å / Num. obs: 134648 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 10.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JAE Resolution: 1.55→14.93 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.036 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NON-PLANAR FAD MOLECULE
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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: 9.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→14.93 Å
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Refine LS restraints |
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