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- PDB-4p7j: Rat apo-COMT sulfate bound -

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Basic information

Entry
Database: PDB / ID: 4p7j
TitleRat apo-COMT sulfate bound
ComponentsCatechol O-methyltransferaseCatechol-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 / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / catechol O-methyltransferase activity ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal filtration / renin secretion into blood stream / dopamine secretion / renal albumin absorption / negative regulation of dopamine metabolic process / response to salt / habituation / artery development / catecholamine metabolic process / S-adenosylmethionine metabolic process / short-term memory / cerebellar cortex morphogenesis / cellular response to phosphate starvation / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / cholesterol efflux / response to temperature stimulus / response to pain / 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 / multicellular organismal response to stress / response to amphetamine / : / learning / kidney development / response to cytokine / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynapse / postsynaptic membrane / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / learning or memory / response to hypoxia / response to xenobiotic stimulus / axon / glutamatergic synapse / dendrite / magnesium ion binding / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 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 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...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 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
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_oper_list.symmetry_operation

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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)24,9083
Polymers24,7721
Non-polymers1352
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.286, 56.286, 119.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: UNP Residues 44-264
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.1 Å / Num. obs: 39464 / % possible obs: 99.8 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.11702 / Net I/σ(I): 10.9261
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.18233 / Mean I/σ(I) obs: 1.8714 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1589) / Classification: refinement
RefinementResolution: 1.45→45.1 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 1974 5 %
Rwork0.1668 --
obs0.1684 39460 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 6 218 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051808
X-RAY DIFFRACTIONf_angle_d1.0852465
X-RAY DIFFRACTIONf_dihedral_angle_d12.024703
X-RAY DIFFRACTIONf_chiral_restr0.073276
X-RAY DIFFRACTIONf_plane_restr0.005319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.33721370.27432628X-RAY DIFFRACTION100
1.4863-1.52650.25711210.232676X-RAY DIFFRACTION100
1.5265-1.57140.22971560.20952621X-RAY DIFFRACTION100
1.5714-1.62210.22051310.19412655X-RAY DIFFRACTION100
1.6221-1.68010.19841290.17572641X-RAY DIFFRACTION100
1.6801-1.74740.19411490.17332652X-RAY DIFFRACTION100
1.7474-1.82690.20611600.17142626X-RAY DIFFRACTION100
1.8269-1.92330.21441410.16462662X-RAY DIFFRACTION100
1.9233-2.04370.19571230.1622690X-RAY DIFFRACTION100
2.0437-2.20150.1741590.15462655X-RAY DIFFRACTION100
2.2015-2.42310.18491360.15892704X-RAY DIFFRACTION100
2.4231-2.77370.20941460.17042705X-RAY DIFFRACTION100
2.7737-3.49430.19891350.16192740X-RAY DIFFRACTION99
3.4943-45.10.17721510.152831X-RAY DIFFRACTION98
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)
15.49832.07192.64273.93551.23675.8173-0.034-0.38740.12450.4775-0.27940.75760.1476-0.63370.24520.22780.03710.09530.1677-0.02470.216-19.771324.592271.2529
24.31032.8563-1.96973.0177-2.80873.4601-0.1317-0.2403-0.06350.56820.114-0.19350.06150.07020.0550.2480.0651-0.00940.1139-0.02390.1333-8.578923.524572.3887
32.2658-0.7634-0.44012.29530.71742.5064-0.0598-0.01580.0010.13560.082-0.02040.0370.0167-0.02650.09020.01420.00320.0599-0.01110.0955-7.360821.42759.3762
41.75620.4855-0.52384.28363.29355.615-0.03810.37110.1122-0.5733-0.10680.2831-0.4107-0.37140.14680.22320.0689-0.02190.18640.01730.2071-12.801626.480847.1174
53.6785-0.0107-0.30351.97180.78052.70460.02740.1953-0.0472-0.2015-0.01960.0399-0.1138-0.157-0.00170.09290.01530.00760.0997-0.02730.089-7.76313.75347.6736
60.47710.11210.6580.8344-0.04816.8325-0.0160.0146-0.10340.0189-0.00050.09250.0716-0.24030.01160.06490.02330.01310.1035-0.01390.1215-3.05683.301655.8609
72.4733-0.581-0.56782.20910.42483.9807-0.11370.3502-0.1127-0.4278-0.0204-0.20670.14260.24330.16540.1509-0.00570.03250.164-0.03680.10411.09628.51745.9627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 261 )

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