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- PDB-5lqk: Crystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)... -

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Basic information

Entry
Database: PDB / ID: 5lqk
TitleCrystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]prop-2-enyl]-2,3-dihydroxy-5-[(4-methylphenyl)methyl]benzamide
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
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
Catechol O-methyltransferase, eukaryotic / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-72M / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of COMT
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5296
Polymers24,6941
Non-polymers8355
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-28 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.424, 85.384, 79.234
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 5 types, 26 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-72M / ~{N}-[(~{E})-3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]prop-2-enyl]-5-[(4-methylphenyl)methyl]-2,3-bis(oxidanyl)benzamide


Mass: 532.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O6
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.24→42.69 Å / Num. obs: 9985 / % possible obs: 84.4 % / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Biso Wilson estimate: 42.685 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.24-2.31.3251.030.423187.5
2.3-2.361.1531.270.509187.3
2.36-2.430.8521.60.579187.4
2.43-2.50.8061.770.659186.4
2.5-2.590.5812.370.742187.1
2.59-2.680.5492.580.804186.1
2.68-2.780.3983.350.891186.2
2.78-2.890.3254.210.898184.8
2.89-3.020.2575.250.948184.9
3.02-3.170.2036.520.958183.2
3.17-3.340.1588.320.978184.2
3.34-3.540.11311.280.989185.1
3.54-3.790.09213.620.991182.5
3.79-4.090.0716.760.994183
4.09-4.480.06718.560.994179.4
4.48-5.010.05719.190.996180
5.01-5.780.06118.540.997179.7
5.78-7.080.0617.840.996177.8
7.08-10.020.04221.850.998176.8
10.02-42.690.02526.510.999172

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMAC5.6.0041refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.24→42.69 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.594 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.308
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES : REFINED INDIVIDUALLY. Data only 80% complete, but ligand density clear
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 440 4.7 %RANDOM
Rwork0.226 ---
obs0.2285 8899 78.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.4 Å2 / Biso mean: 31.557 Å2 / Biso min: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--3.08 Å20 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 2.24→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 55 21 1764
Biso mean--32.55 32.69 -
Num. residues----216
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 30 -
Rwork0.411 613 -
all-643 -
obs--74.59 %

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