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- PDB-4pyn: Humanized rat COMT in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 4pyn
TitleHumanized rat COMT in complex with SAH
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MAGNESIUM / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE
Function / homology
Function and homology information


: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process ...: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / 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 / S-adenosylmethionine metabolic process / renin secretion into blood stream / catecholamine metabolic process / dopamine secretion / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / fear response / short-term memory / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / prostaglandin metabolic process / response to pain / response to food / response to corticosterone / response to temperature stimulus / glycogen metabolic process / negative regulation of dopamine metabolic process / response to stress / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to cytokine / response to amphetamine / learning / kidney development / negative regulation of smooth muscle cell proliferation / female pregnancy / visual learning / response to wounding / response to toxic substance / regulation of blood pressure / response to estrogen / cognition / multicellular organism growth / memory / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / gene expression / vesicle / dendritic spine / postsynaptic membrane / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / 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
: / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Feb 28, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2316
Polymers24,6941
Non-polymers5375
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.316, 61.248, 104.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: unp 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) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical ChemComp-SAH / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→31.75 Å / Num. obs: 67597 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.08501 / Net I/σ(I): 10.2819
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.87944 / Mean I/σ(I) obs: 1.4987 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1448)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→31.75 Å / SU ML: 0.13 / σ(F): 14.6 / Phase error: 13.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1539 3216 5.07 %
Rwork0.1269 --
obs0.1283 67594 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 30 314 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191867
X-RAY DIFFRACTIONf_angle_d1.2262539
X-RAY DIFFRACTIONf_dihedral_angle_d13.811722
X-RAY DIFFRACTIONf_chiral_restr0.071283
X-RAY DIFFRACTIONf_plane_restr0.006328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2002-1.21730.3811230.33272407X-RAY DIFFRACTION92
1.2173-1.23550.32411490.25542669X-RAY DIFFRACTION100
1.2355-1.25480.28141310.22462637X-RAY DIFFRACTION100
1.2548-1.27540.23961530.20042655X-RAY DIFFRACTION100
1.2754-1.29740.24951310.18522640X-RAY DIFFRACTION100
1.2974-1.32090.22761490.17692640X-RAY DIFFRACTION100
1.3209-1.34640.17931150.1672672X-RAY DIFFRACTION100
1.3464-1.37380.21391600.1762643X-RAY DIFFRACTION100
1.3738-1.40370.20311320.15792631X-RAY DIFFRACTION100
1.4037-1.43640.17051340.12252692X-RAY DIFFRACTION100
1.4364-1.47230.15371440.11262635X-RAY DIFFRACTION100
1.4723-1.51210.13671610.10082691X-RAY DIFFRACTION100
1.5121-1.55660.14431320.09712665X-RAY DIFFRACTION100
1.5566-1.60680.13181370.0892663X-RAY DIFFRACTION100
1.6068-1.66420.11441550.08992702X-RAY DIFFRACTION100
1.6642-1.73090.13021460.092658X-RAY DIFFRACTION100
1.7309-1.80960.12571370.09452688X-RAY DIFFRACTION100
1.8096-1.9050.11991450.09482693X-RAY DIFFRACTION100
1.905-2.02440.13531590.09462666X-RAY DIFFRACTION100
2.0244-2.18070.1041470.0992722X-RAY DIFFRACTION100
2.1807-2.40.12931360.10772737X-RAY DIFFRACTION100
2.4-2.74720.14451550.11792729X-RAY DIFFRACTION100
2.7472-3.46040.15941340.13152772X-RAY DIFFRACTION99
3.4604-31.76080.14381630.13922859X-RAY DIFFRACTION98

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