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Yorodumi- PDB-6i3c: Crystal structure of Human soluble catechol O-methyltransferase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i3c | ||||||
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Title | Crystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and S-adensoyl-L-methionine | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / Enzyme / S-adenosyl-L-methionine / Catechol O-methyltransferase | ||||||
Function / homology | Function and homology information Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / developmental process / catechol O-methyltransferase / renal filtration / renal albumin absorption / dopamine secretion / Methylation / habituation / artery development / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / synaptic transmission, dopaminergic / O-methyltransferase activity / cholesterol efflux / response to angiotensin / cellular response to cocaine / exploration behavior / response to food / 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 / response to amphetamine / response to cytokine / methyltransferase activity / multicellular organism growth / visual learning / memory / response to toxic substance / response to wounding / gene expression / methylation / response to oxidative stress / Potential therapeutics for SARS / response to hypoxia / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / dendrite / synapse / magnesium ion binding / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.336 Å | ||||||
Authors | Levy, C.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase. Authors: Czarnota, S. / Johannissen, L.O. / Baxter, N.J. / Rummel, F. / Wilson, A.L. / Cliff, M.J. / Levy, C.W. / Scrutton, N.S. / Waltho, J.P. / Hay, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i3c.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i3c.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i3c ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i3c | 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: 25970.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COMT / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P21964, catechol O-methyltransferase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SAM / |
#4: Chemical | ChemComp-DNC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M Imidazole; MES monohydrate (acid) pH 6.5, 50% v/v pre-cipitant ...Details: 0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M Imidazole; MES monohydrate (acid) pH 6.5, 50% v/v pre-cipitant mix (25% v/v MPD; 25% PEG 1000; 25% PEG 3350) Morpheus condition D4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.336→39.13 Å / Num. obs: 49463 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 10.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Rrim(I) all: 0.097 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 1.336→1.384 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 4891 / CC1/2: 0.824 / Rpim(I) all: 0.27 / Rrim(I) all: 0.45 / % possible all: 99.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse Resolution: 1.336→39.13 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.336→39.13 Å
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Refine LS restraints |
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LS refinement shell |
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