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- PDB-4p7k: Rat COMT in complex with sinefungin -

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Basic information

Entry
Database: PDB / ID: 4p7k
TitleRat COMT in complex with sinefungin
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / S-ADENOSYL-L-METHIONINE / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE
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 / exploration behavior / response to food / 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 / : / learning / kidney development / 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 / cell body / gene expression / 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
ACETATE ION / : / SINEFUNGIN / L(+)-TARTARIC ACID / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.22 Å
AuthorsEhler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Mapping the conformational space accessible to catechol-O-methyltransferase.
Authors: Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)25,4807
Polymers24,7721
Non-polymers7086
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.235, 61.238, 104.802
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 / Catechol-O-methyltransferase


Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: UNP 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) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 5 types, 322 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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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: Jul 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→31.7 Å / Num. obs: 48898 / % possible obs: 75.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.03518 / Net I/σ(I): 28.7269
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.34407 / Mean I/σ(I) obs: 2.4205 / % possible all: 13.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1439) / Classification: refinement
RefinementResolution: 1.22→31.7 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 15.14 / Phase error: 14.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.148 2447 5.01 %
Rwork0.1124 --
obs0.1142 48890 75.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 44 316 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231911
X-RAY DIFFRACTIONf_angle_d1.3092599
X-RAY DIFFRACTIONf_dihedral_angle_d14.302739
X-RAY DIFFRACTIONf_chiral_restr0.073291
X-RAY DIFFRACTIONf_plane_restr0.006337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.24510.3057200.2411286X-RAY DIFFRACTION8
1.2451-1.27220.2305510.1759833X-RAY DIFFRACTION24
1.2722-1.30170.2009820.1341193X-RAY DIFFRACTION34
1.3017-1.33430.1836790.11371562X-RAY DIFFRACTION43
1.3343-1.37040.19111050.10691897X-RAY DIFFRACTION54
1.3704-1.41070.16191240.10262228X-RAY DIFFRACTION63
1.4107-1.45620.15061440.0992616X-RAY DIFFRACTION73
1.4562-1.50830.14391510.09813237X-RAY DIFFRACTION90
1.5083-1.56870.12881890.09183501X-RAY DIFFRACTION98
1.5687-1.64010.15311790.09153562X-RAY DIFFRACTION99
1.6401-1.72650.13121890.09493562X-RAY DIFFRACTION99
1.7265-1.83470.12231690.09973624X-RAY DIFFRACTION99
1.8347-1.97630.12421870.0993590X-RAY DIFFRACTION99
1.9763-2.17520.13181840.09893618X-RAY DIFFRACTION100
2.1752-2.48980.14161800.10753671X-RAY DIFFRACTION100
2.4898-3.13640.14531900.12723675X-RAY DIFFRACTION100
3.1364-31.70.16692240.13383788X-RAY DIFFRACTION98

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