+Open data
-Basic information
Entry | Database: PDB / ID: 4p7g | ||||||
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Title | Rat apo-COMT, phosphate bound | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / S-ADENOSYL-L-METHIONINE / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE | ||||||
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 / Resolution: 2.58 Å | ||||||
Authors | Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Mapping the conformational space accessible to catechol-O-methyltransferase. Authors: Ehler, A. / Benz, J. / Schlatter, D. / 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 | 4p7g.cif.gz | 349.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p7g.ent.gz | 288.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p7g ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p7g | HTTPS FTP |
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-Related structure data
Related structure data | 4p7fC 4p7jC 4p7kC 4pyiC 4pyjC 4pykC 4pylC 4pymC 4pynC 4pyoC 4pyqC C: citing same article (ref.) |
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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: 24772.400 Da / Num. of mol.: 4 / Fragment: UNP residues 44-264 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 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.94 Å3/Da / Density % sol: 58.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: see manuscript |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→48.7 Å / Num. obs: 36241 / % possible obs: 95.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 66.02 Å2 / Rmerge(I) obs: 0.23468 / Net I/σ(I): 16.1347 |
Reflection shell | Resolution: 2.58→2.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.6446 / Mean I/σ(I) obs: 1.5359 / % possible all: 86.5 |
-Processing
Software | Name: BUSTER / Version: 2.11.4 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.58→48.7 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9012 / SU R Cruickshank DPI: 0.482 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.503 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.281
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Displacement parameters | Biso mean: 70.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.486 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.58→48.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.65 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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