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Yorodumi- PDB-2xfn: Human monoamine oxidase B in complex with 2-(2-benzofuranyl)-2- i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xfn | ||||||
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Title | Human monoamine oxidase B in complex with 2-(2-benzofuranyl)-2- imidazoline | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN | ||||||
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 / 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 / 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 / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Bonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / Edmondson, D.E. / Mattevi, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2010 Title: Potentiation of ligand binding through cooperative effects in monoamine oxidase B. Authors: Bonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / Edmondson, D.E. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xfn.cif.gz | 230.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xfn.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/2xfn ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xfn | HTTPS FTP |
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-Related structure data
Related structure data | 2xcgC 2xfoC 2xfpC 2xfqC 2xfuC 1ojaS 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: 58837.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.18 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 164059 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.075 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.222 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJA Resolution: 1.6→68.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.18 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / 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: 15.475 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→68.21 Å
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Refine LS restraints |
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