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Yorodumi- PDB-2zlb: Crystal structure of APO form of rat catechol-O-methyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zlb | ||||||
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Title | Crystal structure of APO form of rat catechol-O-methyltransferase | ||||||
Components | Catechol O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / Alternative initiation / Catecholamine metabolism / Cytoplasm / Magnesium / Membrane / Metal-binding / Phosphoprotein / S-adenosyl-L-methionine / Signal-anchor / Transmembrane / TRANSFERASE (METHYLTRANSFERASE) | ||||||
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 / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / glomerulus development / fear response / multicellular organismal reproductive process / 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 pain / response to corticosterone / prostaglandin metabolic process / 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 / : / learning / response to cytokine / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / response to oxidative stress / response to lipopolysaccharide / dendritic spine / learning or memory / 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: 2.2 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 | 2zlb.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zlb.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zlb_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 2zlb_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2zlb_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 2zlb_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zlb ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zlb | HTTPS FTP |
-Related structure data
Related structure data | 2zthC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24916.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: liver / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus(DE3)RP / References: UniProt: P22734, catechol O-methyltransferase |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M (NH4)2SO4, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 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: Jul 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.16 Å / Num. obs: 11356 / % possible obs: 98.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 34.11 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1565 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VID Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.477 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.22 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.767 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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