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- PDB-4pyj: human apo-COMT, single domain swap -

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Basic information

Entry
Database: PDB / ID: 4pyj
Titlehuman apo-COMT, single domain swap
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CONFORMATIONAL CHANGE / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MEMBRANE / METAL-BINDING / 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 / 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 / habituation / Methylation / artery development / 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 wounding / response to toxic substance / multicellular organism growth / memory / response to oxidative stress / methylation / gene expression / Potential therapeutics for SARS / response to hypoxia / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / dendrite / synapse / 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: 1.9 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

Downloads & links

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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
Water1,27971
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 area5600 Å2
ΔGint-93 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.882, 67.165, 128.827
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


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


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / pH: 8
Details: pH 8.0, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40.359 Å / Num. obs: 18911 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07428 / Net I/σ(I): 10.7626
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.25358 / Mean I/σ(I) obs: 1.2732 / % possible all: 96.4

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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: 1.9→40.359 Å / SU ML: 0.23 / σ(F): 17.62 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 964 5.1 %
Rwork0.1977 --
obs0.2008 18903 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→40.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 3 71 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061647
X-RAY DIFFRACTIONf_angle_d0.9762229
X-RAY DIFFRACTIONf_dihedral_angle_d13.677616
X-RAY DIFFRACTIONf_chiral_restr0.037256
X-RAY DIFFRACTIONf_plane_restr0.004288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.00020.41021480.34522446X-RAY DIFFRACTION96
2.0002-2.12550.32361570.27252493X-RAY DIFFRACTION98
2.1255-2.28960.32291220.2422548X-RAY DIFFRACTION98
2.2896-2.520.27221350.2222540X-RAY DIFFRACTION99
2.52-2.88460.27491370.22032590X-RAY DIFFRACTION99
2.8846-3.63390.29371340.20382590X-RAY DIFFRACTION99
3.6339-40.36810.20391310.15862732X-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)
13.64241.01481.10713.65441.13343.68850.0138-1.8119-0.21590.7276-0.24840.2175-0.2878-0.02320.14080.6244-0.18530.12740.58170.00250.3992-13.582-18.5568-0.3407
22.66090.69570.48734.26541.49285.22620.4677-0.88130.79810.3853-0.44121.5305-0.6484-1.05350.25210.4522-0.21650.13650.5405-0.13660.6159-19.1291-13.8963-8.1721
31.5196-0.3855-0.34811.98450.88784.5990.166-0.10940.39810.0964-0.22540.0644-0.58330.32820.12580.4115-0.11650.02020.55650.0550.4876-11.1962-3.5386-17.4137
43.22110.6558-1.14171.25620.13691.3369-0.11170.122-0.22050.2194-0.03740.22020.092-0.13410.09670.4992-0.110.01670.3413-0.0220.3073-5.6905-17.2708-14.6027
52.9441.1957-0.74471.76670.47341.5119-0.0701-0.0902-0.53350.2526-0.0232-0.14020.65010.04430.01310.5015-0.02380.00970.3371-0.00530.33564.1301-20.8766-17.836
63.5582-0.2323-0.34762.97760.66563.2622-0.08310.2137-0.05310.01230.0017-0.22760.62730.1966-0.01880.3552-0.0961-0.03330.34050.02430.29686.9414-9.1024-16.8425
71.8359-0.4993-0.10632.07520.85022.25220.04630.05080.0911-0.0370.005-0.0007-0.15780.10340.05450.3823-0.0911-0.00290.3610.03070.28123.0524-4.0616-17.9166
82.40310.5380.03732.55010.37393.5074-0.0357-0.0470.44620.07410.16710.1466-0.6108-0.06840.07570.5374-0.0611-0.03510.36520.02540.38251.89093.3038-15.6216
92.38421.77410.57353.23181.42186.4266-0.25730.312-0.3432-0.0690.2497-0.05270.8324-0.0024-0.04210.61350.02870.04860.47890.01190.3611-0.7751-2.720813.8163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 226 )
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 249 )
9X-RAY DIFFRACTION9chain 'A' and (resid 250 through 266 )

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