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- PDB-5p9d: rat catechol O-methyltransferase in complex with 5-(4-fluoropheny... -

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Basic information

Entry
Database: PDB / ID: 5p9d
Titlerat catechol O-methyltransferase in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-(5-imidazol-1-ylpentyl)benzamide at 1.42A
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 / dopamine metabolic process / prostaglandin metabolic process / glycogen 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-77R / (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: 1.42 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 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)25,4686
Polymers24,7721
Non-polymers6955
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.982, 53.958, 80.794
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


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 , 6 types, 255 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-77R / 5-(4-fluorophenyl)-2,3-dihydroxy-N-(5-imidazol-1-ylpentyl)benzamide


Mass: 383.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22FN3O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: 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
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 0.9782 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.42→42.51 Å / Num. obs: 41034 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.121 / Χ2: 0.988 / Net I/σ(I): 9.33 / Num. measured all: 169036
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.42-1.460.9241.3110749303029520.5991.07997.4
1.46-1.50.8371.6410362301128760.6870.98295.5
1.5-1.540.5492.3710777288328350.7760.63798.3
1.54-1.590.4512.8810769282927960.8530.52398.8
1.59-1.640.3783.7210807272026980.890.43599.2
1.64-1.70.344.3610729266226430.920.3999.3
1.7-1.760.2925.2810648257725630.9360.33399.5
1.76-1.830.2346.6710440246524560.9590.26799.6
1.83-1.910.2157.558804237322210.9670.24893.6
1.91-2.010.1499.828131226720690.9780.17391.3
2.01-2.120.1411.939640217021610.9870.15799.6
2.12-2.250.11213.378563207220000.9880.12796.5
2.25-2.40.09115.178030192718570.9910.10396.4
2.4-2.590.08116.838527181118030.9940.09199.6
2.59-2.840.07518.858064168716810.9950.08499.6
2.84-3.180.06121.57254152815170.9960.06999.3
3.18-3.670.05623.75851135513360.9960.06398.6
3.67-4.490.04924.434563116311180.9960.05696.1
4.49-6.350.04625.1940949249160.9980.05299.1
6.35-42.510.0425.4722345585360.9980.04596.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER2.9.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.42→20.69 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.8971 / Cross valid method: THROUGHOUT / σ(F): 0
Details: imidazole flexible, may have ca. 20% conformation outside adenine pocket but was not modeled
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 2012 5.08 %RANDOM
Rwork0.215 ---
obs0.217 39586 86.56 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 111.83 Å2 / Biso mean: 13.57 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.9524 Å20 Å20 Å2
2---0.5058 Å20 Å2
3---2.4582 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: final / Resolution: 1.42→20.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 43 252 1974
Biso mean--14.12 25.07 -
Num. residues----213
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d649SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes272HARMONIC5
X-RAY DIFFRACTIONt_it1825HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2365SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1825HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2490HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion16.6
LS refinement shellResolution: 1.42→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4409 145 4.89 %
Rwork0.4648 2819 -
all0.4636 2964 -
obs--75.33 %

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