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Yorodumi- PDB-2zth: Crystal structure of holo form of rat catechol-o-methyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zth | ||||||
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Title | Crystal structure of holo form of rat catechol-o-methyltransferase | ||||||
Components | Catechol O-methyltransferase | ||||||
Keywords | TRANSFERASE / S-Adenosylmethionine dependent methyltransferase / Alternative initiation / Catecholamine metabolism / Cell membrane / Cytoplasm / Magnesium / Membrane / Metal-binding / Methyltransferase / Neurotransmitter degradation / Phosphoprotein / S-adenosyl-L-methionine / Signal-anchor / Transmembrane | ||||||
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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity ...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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / negative regulation of dopamine metabolic process / renal albumin absorption / catecholamine metabolic process / habituation / artery development / response to salt / short-term memory / S-adenosylmethionine metabolic process / cerebellar cortex morphogenesis / cellular response to phosphate starvation / norepinephrine metabolic process / dopamine catabolic process / glomerulus development / fear response / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / cholesterol efflux / response to temperature stimulus / response to corticosterone / prostaglandin metabolic process / response to pain / glycogen metabolic process / dopamine metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / : / : / behavioral fear response / multicellular organismal response to stress / response to amphetamine / negative regulation of smooth muscle cell proliferation / learning / kidney development / response to cytokine / female pregnancy / regulation of blood pressure / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / cognition / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / methylation / vesicle / response to oxidative stress / postsynapse / response to lipopolysaccharide / learning or memory / dendritic spine / response to hypoxia / response to xenobiotic stimulus / axon / glutamatergic synapse / dendrite / magnesium ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tsuji, E. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: Crystal structures of the Apo and Holo form of rat catechol-O-methyltransferase Authors: Tsuji, E. / Okazaki, K. / Isaji, M. / Takeda, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zth.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zth.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zth_validation.pdf.gz | 697.5 KB | Display | wwPDB validaton report |
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Full document | 2zth_full_validation.pdf.gz | 704.3 KB | Display | |
Data in XML | 2zth_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2zth_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2zth ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2zth | HTTPS FTP |
-Related structure data
Related structure data | 2zlbC 1vidS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 24916.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: liver / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-methyltransferase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SAM / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF THIS ENTITY WAS BASED ON ISOFORM 2 OF UNIPROTKB/SWISS-PROT P22734 (COMT_RAT). UNP- ...THE SEQUENCE OF THIS ENTITY WAS BASED ON ISOFORM 2 OF UNIPROTKB/SWISS-PROT P22734 (COMT_RAT). UNP-RESIDUES 1-43 WERE MISSING IN ISOFORM-2. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M (NH4)2SO4, 26% PEG 8000, 0.2% Sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→52.85 Å / Num. all: 6949 / Num. obs: 6906 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1000 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1vid Resolution: 2.6→39.9 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.401 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / 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: 32.263 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.604→2.672 Å / Total num. of bins used: 20
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