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Yorodumi- PDB-3zyx: Crystal structure of human monoamine oxidase B in complex with me... -
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-Basic information
Entry | Database: PDB / ID: 3zyx | ||||||
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Title | Crystal structure of human monoamine oxidase B in complex with methylene blue and bearing the double mutation I199A-Y326A | ||||||
Components | AMINE OXIDASE [FLAVIN-CONTAINING] B | ||||||
Keywords | OXIDOREDUCTASE / INHIBITOR | ||||||
Function / homology | Function and homology information Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion / : / dopamine catabolic process / primary-amine oxidase / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / dendrite / neuronal cell body / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Milczek, E.M. / Binda, C. / Rovida, S. / Mattevi, A. / Edmondson, D.E. | ||||||
Citation | Journal: FEBS J. / Year: 2011 Title: The 'Gating' Residues Ile199 and Tyr326 in Human Monoamine Oxidase B Function in Substrate and Inhibitor Recognition. Authors: Milczek, E.M. / Binda, C. / Rovida, S. / Mattevi, A. / Edmondson, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zyx.cif.gz | 216.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zyx.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/3zyx ftp://data.pdbj.org/pub/pdb/validation_reports/zy/3zyx | HTTPS FTP |
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-Related structure data
Related structure data | 2v5zS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.525, -0.497, -0.691), Vector: |
-Components
#1: Protein | Mass: 58572.359 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 199 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 326 TO ALA ...ENGINEERED | Sequence details | DISCREPANCIES OCCUR AT SITES 199 AND 326 BECAUSE SITE- DIRECTED MUTAGENESIS HAS BEEN PERFORMED IN ...DISCREPANC | |
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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: 2.74 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 12% PEG4000, 100 MM ADA PH 6.5, 70 MM LITHIUM SULPHATE, 8.5 MM ZWITTERGENT 3-12 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 64424 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5Z Resolution: 2.2→43.31 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.036 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.2 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.776 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→43.31 Å
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