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- PDB-3hvi: Rat catechol O-methyltransferase in complex with a catechol-type,... -

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Basic information

Entry
Database: PDB / ID: 3hvi
TitleRat catechol O-methyltransferase in complex with a catechol-type, N6-ethyladenine-containing bisubstrate inhibitor
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / Alternative initiation / Catecholamine metabolism / Cell membrane / Magnesium / Membrane / Metal-binding / Phosphoprotein / S-adenosyl-L-methionine / Signal-anchor / Transmembrane
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-619 / (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. / Schlatter, D. / Stihle, M. / Benz, J. / Rudolph, M.G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.
Authors: Ellermann, M. / Jakob-Roetne, R. / Lerner, C. / Borroni, E. / Schlatter, D. / Roth, D. / Ehler, A. / Rudolph, M.G. / Diederich, F.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Database references / Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)25,5586
Polymers24,7721
Non-polymers7865
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.857, 54.706, 80.617
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, UNP RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Plasmid: pDS56/RBSII / 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, 330 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-619 / N-[(E)-3-[(2R,3S,4R,5R)-5-(6-ethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide


Mass: 550.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27FN6O6
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 8000, 0.1M BT pH 5.5, 0.1M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→33.5 Å / Num. obs: 68810 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 14343 / Rsym value: 0.58 / % possible all: 94.4

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Processing

Software
NameVersionClassification
COMOphasing
REFMAC5.5.0088refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→32.45 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.21 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1614 3331 5 %RANDOM
Rwork0.13064 ---
obs0.13216 62693 94.14 %-
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: 10.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.74 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 51 325 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221943
X-RAY DIFFRACTIONr_bond_other_d0.0020.021326
X-RAY DIFFRACTIONr_angle_refined_deg1.9262.0142672
X-RAY DIFFRACTIONr_angle_other_deg1.03933277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35224.71387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5915355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0951512
X-RAY DIFFRACTIONr_chiral_restr0.1520.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212177
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02380
X-RAY DIFFRACTIONr_mcbond_it1.8041.51149
X-RAY DIFFRACTIONr_mcbond_other0.8731.5460
X-RAY DIFFRACTIONr_mcangle_it2.56821883
X-RAY DIFFRACTIONr_scbond_it3.5493794
X-RAY DIFFRACTIONr_scangle_it4.944.5767
X-RAY DIFFRACTIONr_rigid_bond_restr1.64233269
X-RAY DIFFRACTIONr_sphericity_free10.1453334
X-RAY DIFFRACTIONr_sphericity_bonded4.4333205
LS refinement shellResolution: 1.197→1.228 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 213 -
Rwork0.274 3845 -
obs--79.62 %

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