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Yorodumi- PDB-3u81: Crystal structure of a SAH-bound semi-holo form of rat Catechol-O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u81 | ||||||
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Title | Crystal structure of a SAH-bound semi-holo form of rat Catechol-O-methyltransferase | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process / response to salt / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / developmental process / catechol O-methyltransferase / renal filtration / renal albumin absorption / dopamine secretion / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / habituation / artery development / catecholamine metabolic process / short-term memory / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / cholesterol efflux / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / response to pain / response to temperature stimulus / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / multicellular organismal response to stress / response to amphetamine / learning / kidney development / response to organic substance / response to cytokine / female pregnancy / negative regulation of smooth muscle cell proliferation / multicellular organism growth / visual learning / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynaptic membrane / postsynapse / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / response to hypoxia / learning or memory / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||
Authors | Ehler, A. / Schlatter, D. / Stihle, M. / Benz, J. / Rudolph, M.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Catechol-O-methyltransferase in complex with substituted 3'-deoxyribose bisubstrate inhibitors. Authors: Ellermann, M. / Lerner, C. / Burgy, G. / Ehler, A. / Bissantz, C. / Jakob-Roetne, R. / Paulini, R. / Allemann, O. / Tissot, H. / Grunstein, D. / Stihle, M. / Diederich, F. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u81.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u81.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/3u81 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/3u81 | HTTPS FTP |
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-Related 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: 24694.332 Da / Num. of mol.: 1 / Fragment: unp residues 44-264 / Mutation: M134I, Y138C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
Sequence details | THE DATABASE REFERENCE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.3M Na-malonate pH 7.0, 0.1M hepes/NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: DECTRIS / Detector: PIXEL / Date: Jun 17, 2011 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.13→39.81 Å / Num. obs: 79382 / % possible obs: 97.4 % / Redundancy: 6.14 % / Rmerge(I) obs: 0.0845 / Rsym value: 0.0845 / Net I/σ(I): 8.88 | |||||||||
Reflection shell | Resolution: 1.13→1.23 Å / Redundancy: 5.78 % / Rmerge(I) obs: 0.7142 / Mean I/σ(I) obs: 1.49 / Rsym value: 0.7142 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→39.81 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 15.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.36 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.13→39.81 Å
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Refine LS restraints |
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LS refinement shell |
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