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- PDB-4pyi: human apo COMT -

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Basic information

Entry
Database: PDB / ID: 4pyi
Titlehuman apo COMT
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CONFORMATIONAL CHANGE / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MEMBRANE / METAL-BINDING / SIGNAL-ANCHOR
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / renal sodium excretion ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / renin secretion into blood stream / dopamine secretion / renal albumin absorption / Methylation / artery development / habituation / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / synaptic transmission, dopaminergic / cellular response to phosphate starvation / O-methyltransferase activity / cellular response to cocaine / cholesterol efflux / prostaglandin metabolic process / response to food / response to corticosterone / glycogen metabolic process / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / response to cytokine / response to amphetamine / methyltransferase activity / visual learning / response to toxic substance / response to wounding / multicellular organism growth / memory / methylation / response to oxidative stress / Potential therapeutics for SARS / gene expression / response to hypoxia / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / synapse / dendrite / magnesium ion binding / extracellular exosome / membrane / plasma 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
Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 / Refinement description / Category: diffrn_detector / software / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)24,5012
Polymers24,4781
Non-polymers231
Water2,396133
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.596, 42.638, 43.663
Angle α, β, γ (deg.)115.03, 95.35, 108.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24478.076 Da / Num. of mol.: 1 / Fragment: soluble form, unp resideus 51-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMT / Production host: Escherichia coli (E. coli) / References: UniProt: P21964, catechol O-methyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / pH: 7
Details: pH 7.0, 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 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→28.8 Å / Num. obs: 38358 / % possible obs: 92.8 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 1.202 / % possible all: 56.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1491)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE MODEL

Resolution: 1.35→28.77 Å / SU ML: 0.19 / σ(F): 1.97 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1921 5.01 %
Rwork0.162 --
obs0.165 38318 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 1 133 1745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091704
X-RAY DIFFRACTIONf_angle_d1.2332320
X-RAY DIFFRACTIONf_dihedral_angle_d13.87655
X-RAY DIFFRACTIONf_chiral_restr0.07268
X-RAY DIFFRACTIONf_plane_restr0.006300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38380.361140.33462192X-RAY DIFFRACTION78
1.3838-1.42120.32071390.25632559X-RAY DIFFRACTION92
1.4212-1.4630.31481520.23872544X-RAY DIFFRACTION92
1.463-1.51020.29371440.22092644X-RAY DIFFRACTION93
1.5102-1.56420.29441300.19322584X-RAY DIFFRACTION93
1.5642-1.62680.21331260.15812648X-RAY DIFFRACTION95
1.6268-1.70090.23181380.14612689X-RAY DIFFRACTION95
1.7009-1.79050.19841400.14522675X-RAY DIFFRACTION95
1.7905-1.90270.19551430.13922671X-RAY DIFFRACTION96
1.9027-2.04950.22351330.14562670X-RAY DIFFRACTION95
2.0495-2.25570.17921440.14222678X-RAY DIFFRACTION95
2.2557-2.5820.18241440.14142725X-RAY DIFFRACTION97
2.582-3.25230.21500.15172718X-RAY DIFFRACTION98
3.2523-28.78020.18531240.16152400X-RAY DIFFRACTION85

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