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- PDB-5lqn: Crystal Structure of COMT in complex with 2-[(3-chlorophenoxy)met... -

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Basic information

Entry
Database: PDB / ID: 5lqn
TitleCrystal Structure of COMT in complex with 2-[(3-chlorophenoxy)methyl]-4-methyl-5-(1H-pyrazol-5-yl)-1,3-thiazole
ComponentsCatechol O-methyltransferaseCatechol-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 / 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
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-72O / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of COMT in complex with 2-[(3-chlorophenoxy)methyl]-4-methyl-5-(1H-pyrazol-5-yl)-1,3-thiazole
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release

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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)25,0002
Polymers24,6941
Non-polymers3061
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.186, 59.945, 78.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase / 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical ChemComp-72O / 2-[(3-chloranylphenoxy)methyl]-4-methyl-5-(1~{H}-pyrazol-5-yl)-1,3-thiazole


Mass: 305.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→47.65 Å / Num. obs: 24349 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 39.176 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.51
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.72-1.761.3791.30.5721100
1.76-1.811.1841.640.72199.8
1.81-1.870.942.110.805199.6
1.87-1.920.5363.540.905199.9
1.92-1.990.3725.210.943199.9
1.99-2.060.2816.70.9651100
2.06-2.130.2118.930.981100
2.13-2.220.1810.170.984199.8
2.22-2.320.13713.360.992199.9
2.32-2.430.09816.460.996199.8
2.43-2.560.08918.650.996199.9
2.56-2.720.072220.996199.9
2.72-2.910.06323.990.997199.8
2.91-3.140.05328.960.998199.9
3.14-3.440.04932.270.997199.7
3.44-3.850.04434.910.998199.7
3.85-4.440.04134.450.998198.9
4.44-5.440.03837.230.999199.6
5.44-7.690.03435.170.999199.6
7.69-47.650.02635.760.999199.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMAC5.6.0081refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.72→47.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.144 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124
Details: 3-Chloro-phenoxymethyl not well defined by electron density; could be mixture of 2-(3-Chloro-phenoxymethyl)-4-methyl-5-(2H-pyrazol-3-yl)-thiazole and molecule derived from starting material, ...Details: 3-Chloro-phenoxymethyl not well defined by electron density; could be mixture of 2-(3-Chloro-phenoxymethyl)-4-methyl-5-(2H-pyrazol-3-yl)-thiazole and molecule derived from starting material, e.g. 4-methyl-5-(2H-pyrazol-3-yl)-thiazole. orientation of chloro-substituent rather certain.
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1195 5.2 %RANDOM
Rwork0.1964 ---
obs0.1988 22006 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80 Å2 / Biso mean: 36.19 Å2 / Biso min: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.72→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 20 116 1809
Biso mean--50.57 45.43 -
Num. residues----213
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 78 -
Rwork0.361 1488 -
all-1566 -
obs--86.95 %

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