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- PDB-4p7f: Mouse apo-COMT -

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Basic information

Entry
Database: PDB / ID: 4p7f
TitleMouse apo-COMT
ComponentsCatechol 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 / Methylation / catechol-containing compound metabolic process / norepinephrine secretion / response to dopamine / mastication / catechol O-methyltransferase activity / catechol O-methyltransferase / renal sodium excretion ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / catechol-containing compound metabolic process / norepinephrine secretion / response to dopamine / mastication / catechol O-methyltransferase activity / catechol O-methyltransferase / renal sodium excretion / renal filtration / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / response to salt / dopamine catabolic process / glomerulus development / norepinephrine metabolic process / fear response / synaptic transmission, dopaminergic / cellular response to phosphate starvation / response to angiotensin / cellular response to cocaine / exploration behavior / cholesterol efflux / response to food / prostaglandin metabolic process / response to corticosterone / response to temperature stimulus / glycogen metabolic process / response to stress / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / learning / kidney development / visual learning / multicellular organism growth / regulation of blood pressure / memory / response to wounding / cognition / response to toxic substance / gene expression / methylation / vesicle / response to oxidative stress / learning or memory / response to hypoxia / response to xenobiotic stimulus / synapse / magnesium ion binding / mitochondrion / 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
HYDROGENPHOSPHATE ION / PHOSPHATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 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 13, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Advisory / Data collection ...Advisory / 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 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / 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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _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_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)25,3398
Polymers24,7441
Non-polymers5957
Water3,351186
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)50,67916
Polymers49,4892
Non-polymers1,19014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4560 Å2
ΔGint-67 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.822, 123.822, 88.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-406-

HOH

31A-467-

HOH

41A-484-

HOH

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24744.455 Da / Num. of mol.: 1 / Fragment: UNP Residues 44-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Comt, Comt1 / Production host: Escherichia coli (E. coli) / References: UniProt: O88587, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO4P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
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: 0.9998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.37→40.8 Å / Num. obs: 54274 / % possible obs: 99.7 % / Redundancy: 10 % / Rmerge(I) obs: 0.06922 / Net I/σ(I): 14.8069
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.024 / Mean I/σ(I) obs: 0.864 / % possible all: 99.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.37→40.8 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 2750 5.07 %
Rwork0.1235 --
obs0.1258 54222 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 31 186 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081830
X-RAY DIFFRACTIONf_angle_d1.2122504
X-RAY DIFFRACTIONf_dihedral_angle_d13.665703
X-RAY DIFFRACTIONf_chiral_restr0.079279
X-RAY DIFFRACTIONf_plane_restr0.006324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.39360.38041310.38072533X-RAY DIFFRACTION98
1.3936-1.4190.3671370.30212529X-RAY DIFFRACTION99
1.419-1.44630.35221270.2672562X-RAY DIFFRACTION99
1.4463-1.47580.26121270.23722562X-RAY DIFFRACTION100
1.4758-1.50790.27391580.19922522X-RAY DIFFRACTION99
1.5079-1.5430.26081430.17912555X-RAY DIFFRACTION100
1.543-1.58160.21921340.16372565X-RAY DIFFRACTION99
1.5816-1.62430.20981370.14852547X-RAY DIFFRACTION99
1.6243-1.67210.20581310.12852565X-RAY DIFFRACTION100
1.6721-1.72610.18861430.12552560X-RAY DIFFRACTION100
1.7261-1.78780.15091450.11022556X-RAY DIFFRACTION100
1.7878-1.85940.16381310.09982575X-RAY DIFFRACTION100
1.8594-1.9440.13871400.0912574X-RAY DIFFRACTION100
1.944-2.04650.13771310.09162579X-RAY DIFFRACTION100
2.0465-2.17470.14121290.09472597X-RAY DIFFRACTION100
2.1747-2.34260.14641630.09722570X-RAY DIFFRACTION100
2.3426-2.57830.13371420.10012604X-RAY DIFFRACTION100
2.5783-2.95130.15361370.11642585X-RAY DIFFRACTION100
2.9513-3.71790.17891300.12342637X-RAY DIFFRACTION100
3.7179-40.87060.16541340.12452695X-RAY DIFFRACTION100

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