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- PDB-4pyk: human COMT, double domain swap -

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Basic information

Entry
Database: PDB / ID: 4pyk
Titlehuman COMT, double domain swap
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CONFORMATIONAL CHANGE / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MAGNESIUM / MEMBRANE / METAL-BINDING / S-ADENOSYL-L-METHIONINE / SIGNAL-ANCHOR / ENZYME
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 / 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 / renal sodium excretion / : / : / catechol O-methyltransferase / developmental process / renal filtration / renin secretion into blood stream / dopamine secretion / Methylation / renal albumin absorption / response to salt / habituation / artery development / cerebellar cortex morphogenesis / cellular response to phosphate starvation / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / synaptic transmission, dopaminergic / O-methyltransferase activity / response to angiotensin / cellular response to cocaine / exploration behavior / response to food / cholesterol efflux / 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 / response to amphetamine / methyltransferase activity / response to cytokine / visual learning / multicellular organism growth / response to toxic substance / memory / response to wounding / gene expression / methylation / response to oxidative stress / Potential therapeutics for SARS / 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 / 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
Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
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_atom_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_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.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

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5614
Polymers24,4781
Non-polymers833
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catechol O-methyltransferase
hetero molecules

A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1228
Polymers48,9562
Non-polymers1656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9850 Å2
ΔGint-128 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.786, 66.825, 128.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

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Components

#1: Protein Catechol O-methyltransferase / Catechol-O-methyltransferase


Mass: 24478.076 Da / Num. of mol.: 1 / Fragment: unp residues 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / pH: 7.5
Details: pH 7.5, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→40.222 Å / Num. obs: 78926 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1041 / Net I/σ(I): 11.5483
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.17196 / Mean I/σ(I) obs: 1.5281 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1439)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2.22→40.222 Å / SU ML: 0.29 / σ(F): 22.8 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 571 4.78 %
Rwork0.1725 --
obs0.176 11947 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→40.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 3 50 1723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221713
X-RAY DIFFRACTIONf_angle_d1.2222335
X-RAY DIFFRACTIONf_dihedral_angle_d15.887634
X-RAY DIFFRACTIONf_chiral_restr0.038263
X-RAY DIFFRACTIONf_plane_restr0.005298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2201-2.44350.31331380.26262774X-RAY DIFFRACTION100
2.4435-2.7970.36041190.24132840X-RAY DIFFRACTION100
2.797-3.52360.2871570.18492819X-RAY DIFFRACTION100
3.5236-40.2290.19131570.13622943X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1818-1.5834-0.20414.33521.42423.5664-0.29110.8357-0.9165-0.167-0.23230.96310.5974-0.33250.4410.45830.1005-0.01590.5569-0.0980.6682-16.991213.70212.5052
24.59890.6988-0.88562.0494-0.49482.8825-0.07950.1892-0.2602-0.0524-0.04990.16130.4219-0.28920.1290.3752-0.0943-0.03040.27440.00160.3038-2.9713-15.2564-16.5075
30.2013-0.356-0.31120.70421.37237.0694-0.0715-0.0251-0.0250.19110.0679-0.0245-0.0555-0.22770.07910.3076-0.0846-0.010.26790.05030.29893.3189-1.8217-9.076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 193 )
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 266 )

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