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Yorodumi- PDB-2z5y: Crystal Structure of Human Monoamine Oxidase A (G110A) with Harmine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z5y | ||||||
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Title | Crystal Structure of Human Monoamine Oxidase A (G110A) with Harmine | ||||||
Components | Amine oxidase [flavin-containing] A | ||||||
Keywords | OXIDOREDUCTASE / HUMAN MONOAMINE OXIDASE A / MUTANT / G110A / FAD / HARMINE / DIMETHYLDECYLPHOSPHINE OXIDE / SINGLE HELIX TRANS-MEMBRANE PROTEIN / Acetylation / Catecholamine metabolism / Flavoprotein / Mitochondrion / Neurotransmitter degradation / Polymorphism / Transmembrane | ||||||
Function / homology | Function and homology information Dopamine clearance from the synaptic cleft / Defective MAOA causes BRUNS / biogenic amine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Metabolism of serotonin / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / positive regulation of signal transduction ...Dopamine clearance from the synaptic cleft / Defective MAOA causes BRUNS / biogenic amine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Metabolism of serotonin / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / positive regulation of signal transduction / Norepinephrine Neurotransmitter Release Cycle / aliphatic amine oxidase activity / dopamine catabolic process / primary-amine oxidase / primary amine oxidase activity / flavin adenine dinucleotide binding / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Son, S.Y. / Ma, J. / Yoshimura, M. / Tsukihara, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structure of human monoamine oxidase A at 2.2-A resolution: The control of opening the entry for substrates/inhibitors Authors: Son, S.Y. / Ma, J. / Kondou, Y. / Yoshimura, M. / Yamashita, E. / Tsukihara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5y.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5y.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 2z5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z5y_validation.pdf.gz | 740 KB | Display | wwPDB validaton report |
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Full document | 2z5y_full_validation.pdf.gz | 750.7 KB | Display | |
Data in XML | 2z5y_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 2z5y_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5y ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5y | HTTPS FTP |
-Related structure data
Related structure data | 2z5xC 1o5wS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58271.867 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-524 / Mutation: G110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: YEp51 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: P21397, monoamine oxidase | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-HRM / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.6M AMMONIUM SULFATE, 100mM CITRIC ACID, pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→49.57 Å / Num. all: 87380 / Num. obs: 31614 / % possible obs: 71.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 24.258 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.16→2.25 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1454 / % possible all: 21.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O5W Resolution: 2.17→44.24 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.254 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.229 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.594 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→44.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.168→2.224 Å / Total num. of bins used: 20
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