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- PDB-5pa6: humanized rat COMT in complex with 7-(4-fluorophenyl)quinoxalin-5-ol -

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Basic information

Entry
Database: PDB / ID: 5pa6
Titlehumanized rat COMT in complex with 7-(4-fluorophenyl)quinoxalin-5-ol
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
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 / 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 / catecholamine catabolic process / catechol-containing compound metabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal filtration / renin secretion into blood stream / dopamine secretion / renal albumin absorption / negative regulation of dopamine metabolic process / response to salt / habituation / artery development / catecholamine metabolic process / S-adenosylmethionine metabolic process / short-term memory / cerebellar cortex morphogenesis / cellular response to phosphate starvation / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / response to food / exploration behavior / cholesterol efflux / response to temperature stimulus / response to pain / response to corticosterone / dopamine metabolic process / glycogen metabolic process / prostaglandin 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 / : / kidney development / learning / response to cytokine / 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 / methylation / postsynapse / postsynaptic membrane / response to oxidative stress / vesicle / 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
7-(4-fluorophenyl)quinoxalin-5-ol / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a COMT complex
Authors: Lerner, C. / Jakob-Roetne, R. / Groebke-Zbinden, K. / Buettelmann, B. / Rudolph, M.G.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6827
Polymers24,6941
Non-polymers9886
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.743, 55.863, 78.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase / Catechol-O-methyltransferase / Humanized rat COMT


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264 / Mutation: M134I, Y138C
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

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Non-polymers , 7 types, 194 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-7JW / 7-(4-fluorophenyl)quinoxalin-5-ol


Mass: 240.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9FN2O
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
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 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.31→45.57 Å / Num. obs: 55858 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.12 % / Biso Wilson estimate: 21.558 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.092 / Rsym value: 0.072 / Χ2: 1.027 / Net I/σ(I): 10.62 / Num. measured all: 342108
Reflection shellResolution: 1.31→1.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.29 / Num. measured obs: 4634 / Num. possible: 747 / Num. unique obs: 743 / CC1/2: 0.998 / Rrim(I) all: 0.034 / Rsym value: 0.751 / Rejects: 0 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.29→42.66 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.258 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 2635 5 %RANDOM
Rwork0.1701 ---
obs0.1712 49658 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.48 Å2 / Biso mean: 16.528 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.29→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 64 189 1926
Biso mean--17.8 28.34 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021831
X-RAY DIFFRACTIONr_bond_other_d0.0020.021771
X-RAY DIFFRACTIONr_angle_refined_deg1.2472.0242498
X-RAY DIFFRACTIONr_angle_other_deg0.88234096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0055232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47724.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43115326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1331511
X-RAY DIFFRACTIONr_chiral_restr0.0740.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_mcbond_it0.6641.448874
X-RAY DIFFRACTIONr_mcbond_other0.6641.448873
X-RAY DIFFRACTIONr_mcangle_it0.8782.1721094
X-RAY DIFFRACTIONr_rigid_bond_restr0.66433602
X-RAY DIFFRACTIONr_sphericity_free23.646556
X-RAY DIFFRACTIONr_sphericity_bonded4.42853695
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 168 -
Rwork0.364 3160 -
all-3328 -
obs--79.69 %

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