+Open data
-Basic information
Entry | Database: PDB / ID: 2xfu | |||||||||
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Title | Human monoamine oxidase B with tranylcypromine | |||||||||
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 / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity / dopamine catabolic process / primary methylamine oxidase activity / 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 / neuronal cell body / dendrite / mitochondrion / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Binda, C. / Li, M. / Hubalek, F. / Restelli, N. / 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. #1: 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 | 2xfu.cif.gz | 218.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xfu.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xfu_validation.pdf.gz | 948.7 KB | Display | wwPDB validaton report |
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Full document | 2xfu_full_validation.pdf.gz | 955.9 KB | Display | |
Data in XML | 2xfu_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 2xfu_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/2xfu ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xfu | HTTPS FTP |
-Related structure data
Related structure data | 2xcgC 2xfnC 2xfoC 2xfpC 2xfqC 1ojb 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.528, -0.497, -0.688), Vector: |
-Components
#1: Protein | Mass: 58706.531 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: Water | ChemComp-HOH / | Nonpolymer details | FLAVIN ADENINE DINUCLEOTIDE (FA8): IN BOTH CHAIN A AND CHAIN B, THE C4A ATOM OF THE FA8 MOLECULE IS ...FLAVIN ADENINE DINUCLEOTI | |
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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: 2.6 Å3/Da / Density % sol: 53 % / 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: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 64040 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJB 1ojb Resolution: 2.2→14.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.316 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.196 / 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: 25.564 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→14.99 Å
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