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- PDB-5p99: rat catechol O-methyltransferase in complex with N-[2-[2-(3,4-dih... -

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Basic information

Entry
Database: PDB / ID: 5p99
Titlerat catechol O-methyltransferase in complex with N-[2-[2-(3,4-dihydroxyphenyl)-2-oxoethyl]sulfanylethyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.20A
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 / catecholamine catabolic process / catechol O-methyltransferase activity / 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 O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / dopamine secretion / renin secretion into blood stream / negative regulation of dopamine metabolic process / fear response / catecholamine metabolic process / renal albumin absorption / artery development / habituation / short-term memory / cerebellar cortex morphogenesis / S-adenosylmethionine metabolic process / response to salt / dopamine catabolic process / cellular response to phosphate starvation / glomerulus development / norepinephrine metabolic process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / response to stress / response to food / exploration behavior / response to temperature stimulus / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / response to pain / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / kidney development / learning / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / vesicle / postsynapse / methylation / 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 / Class I-like SAM-dependent O-methyltransferase / 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-77M / (4S,5S)-1,2-DITHIANE-4,5-DIOL / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a COMT complex
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _refine.B_iso_max / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_number_measured_all / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.2Nov 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 2.3Apr 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)25,7818
Polymers24,7721
Non-polymers1,0087
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.992, 53.941, 80.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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


Mass: 24772.400 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

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Non-polymers , 7 types, 310 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-77M / N-[2-[2-(3,4-dihydroxyphenyl)-2-oxoethyl]sulfanylethyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide


Mass: 457.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20FNO6S
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.2→42.51 Å / Num. obs: 67120 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.55 % / Biso Wilson estimate: 17.06 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.92
Reflection shellResolution: 1.2→1.23 Å / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 1.27 / % possible all: 85.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0088refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE MODEL

Resolution: 1.2→42.51 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.272 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3291 5 %RANDOM
Rwork0.146 ---
obs0.147 62115 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 61 303 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221824
X-RAY DIFFRACTIONr_bond_other_d0.0040.021207
X-RAY DIFFRACTIONr_angle_refined_deg1.9052.0222488
X-RAY DIFFRACTIONr_angle_other_deg1.05732976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86324.93577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76115323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.433159
X-RAY DIFFRACTIONr_chiral_restr0.1330.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0441.51092
X-RAY DIFFRACTIONr_mcbond_other0.8911.5440
X-RAY DIFFRACTIONr_mcangle_it2.9721774
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3523732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1184.5704
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.01133031
X-RAY DIFFRACTIONr_sphericity_free11.0073307
X-RAY DIFFRACTIONr_sphericity_bonded4.18732988
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 179 -
Rwork0.352 3553 -
obs--74.89 %

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