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Yorodumi- PDB-2c72: Functional Role of the Aromatic Cage in Human Monoamine Oxidase B... -
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-Basic information
Entry | Database: PDB / ID: 2c72 | ||||||
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Title | Functional Role of the Aromatic Cage in Human Monoamine Oxidase B: Structures and Catalytic Properties of Tyr435 Mutant Proteins | ||||||
Components | AMINE OXIDASE (FLAVIN-CONTAINING) B | ||||||
Keywords | OXIDOREDUCTASE / ENANTIOSELECTIVITY / FAD / FLAVIN / FLAVOPROTEIN / HUMAN MONOAMINE OXIDASE / INHIBITOR BINDING / MITOCHONDRION / RASAGILINE / TRANSMEMBRANE / PARKINSON | ||||||
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 Å | ||||||
Authors | Li, M. / Binda, C. / Mattevi, A. / Edmondson, D.E. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Functional Role of the Aromatic Cage in Human Monoamine Oxidase B: Structures and Catalytic Properties of Tyr435 Mutant Proteins Authors: Li, M. / Binda, C. / 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 | 2c72.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c72.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c72_validation.pdf.gz | 953.6 KB | Display | wwPDB validaton report |
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Full document | 2c72_full_validation.pdf.gz | 966.5 KB | Display | |
Data in XML | 2c72_validation.xml.gz | 40 KB | Display | |
Data in CIF | 2c72_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c72 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c72 | HTTPS FTP |
-Related structure data
Related structure data | 2c70C 2c73C 2c75C 2c76C 1s2qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
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-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (-0.5284, -0.4977, -0.6878), Vector: |
-Components
#1: Protein | Mass: 58812.707 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) / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 434 TO HIS ENGINEERED RESIDUE IN CHAIN B, TYR 434 TO HIS THE ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.07 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 83429 / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S2Q Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.331 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.152 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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