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- PDB-5lqj: Crystal Structure of COMT in complex with 3-cyclopropyl-5-methyl-... -

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Basic information

Entry
Database: PDB / ID: 5lqj
TitleCrystal Structure of COMT in complex with 3-cyclopropyl-5-methyl-4-phenyl-1,2,4-triazole
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
Function / homology
Function and homology information


positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / habituation / artery development / short-term memory / 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 / estrogen metabolic process / exploration behavior / cholesterol efflux / response to food / prostaglandin metabolic process / response to corticosterone / response to temperature stimulus / response to pain / 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 / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / : / response to wounding / regulation of blood pressure / memory / cognition / response to toxic substance / response to estrogen / cell body / gene expression / methylation / vesicle / postsynaptic membrane / response to lipopolysaccharide / dendritic spine / response to oxidative stress / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / 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
3-cyclopropyl-5-methyl-4-phenyl-1,2,4-triazole / : / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of COMT in complex with 3-cyclopropyl-5-methyl-4-phenyl-1,2,4-triazole
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,91714
Polymers98,7774
Non-polymers1,14010
Water2,270126
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9173
Polymers24,6941
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules

D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8857
Polymers49,3892
Non-polymers4965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
3
D: Catechol O-methyltransferase
hetero molecules

B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8857
Polymers49,3892
Non-polymers4965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
4
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1164
Polymers24,6941
Non-polymers4213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.184, 170.184, 68.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 4 / Fragment: SOLUBLE FORM, RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-72N / 3-cyclopropyl-5-methyl-4-phenyl-1,2,4-triazole


Mass: 199.252 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H13N3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→120.3 Å / Num. obs: 39635 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 57.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.217 / Net I/σ(I): 11.21
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.41-2.472.9611.040.357199.9
2.47-2.542.4871.250.44199.9
2.54-2.612.121.480.565199.9
2.61-2.691.711.870.6651100
2.69-2.781.3752.360.741199.7
2.78-2.881.0173.20.845199.9
2.88-2.990.83740.8861100
2.99-3.110.6195.690.9481100
3.11-3.250.418.20.9721100
3.25-3.410.29910.940.9831100
3.41-3.590.22113.870.991199.9
3.59-3.810.17616.020.993199.9
3.81-4.070.12821.080.9961100
4.07-4.40.09826.320.998199.9
4.4-4.820.08529.070.998199.9
4.82-5.390.08926.410.998199.9
5.39-6.220.09225.270.998199.8
6.22-7.620.07530.070.9981100
7.62-10.780.04540.020.999199.8
10.78-120.340.04241.360.999197.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.41→47.201 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.83
Details: ligand does not bind at the active site but acts as an additive for crystallization. Two of the four molecules in the a.u. have their C-terminal beta-strand domain-swapped.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1979 5 %random
Rwork0.1738 ---
obs0.177 39577 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.54 Å2 / Biso mean: 56.9636 Å2 / Biso min: 26.12 Å2
Refinement stepCycle: final / Resolution: 2.41→47.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 80 126 6916
Biso mean--54.49 49.26 -
Num. residues----855
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)
16.8270.0059-3.36051.6570.90914.29120.12230.60390.4762-0.0543-0.0177-0.1442-0.49930.1934-0.07470.3426-0.0073-0.06490.47110.03570.40576.8446-35.1516-40.1453
20.2277-0.16380.40271.578-1.52811.7409-0.0066-0.1375-0.1234-0.2943-0.0026-0.08870.2212-0.16780.0710.3485-0.00060.01870.44330.0380.46363.7794-49.1232-36.074
32.2827-0.82891.09212.6295-0.55951.287-0.2281-0.07750.14530.13970.192-0.3463-0.0154-0.04890.02880.37040.0399-0.00540.4027-0.0670.377214.7088-46.0167-24.8041
42.4167-0.82630.00852.3524-0.38513.225-0.1342-0.2430.08350.02110.2933-0.0760.28380.1804-0.12650.34340.03840.01710.3499-0.00380.368621.149-60.6025-30.8295
52.0978-0.0665-0.02972.7253-0.93227.1301-0.03580.1264-0.30990.38760.12110.1899-0.3087-0.154-0.11440.43030.0172-0.03070.34750.00960.401715.0481-61.7552-35.6393
64.37542.6744-0.29685.83-0.23993.09750.68540.43811.3340.6903-0.5151.082-0.3481-0.3807-0.00720.63680.07530.00780.59560.05730.9939-7.3096-20.31921.7024
73.6803-0.5280.13240.6973-0.21820.6128-0.26-0.24330.52290.276-0.15430.2352-0.1805-0.1770.36670.62820.029-0.02070.4435-0.1070.66895.1129-24.61699.4661
81.9945-0.1258-0.03751.80950.29652.1616-0.09980.45840.1706-0.14630.15140.1478-0.2599-0.23-0.0480.3756-0.0561-0.02010.48480.0760.37375.7783-31.3675-4.7746
92.1327-0.2238-0.38211.1310.30562.01960.0834-0.0266-0.0137-0.0516-0.0198-0.1257-0.07410.1248-0.02660.32870.00480.00320.36940.02050.365313.4544-39.64567.3192
101.3362-0.8590.74571.69940.96682.2671-0.26310.1379-0.0328-0.5609-0.0824-0.70960.0641-0.07420.54240.4060.04530.03890.26120.07850.5005-15.9128-34.270728.8612
116.80930.1398-3.10912.4315-1.13385.29450.1344-0.10580.57140.1731-0.03730.3074-0.6114-0.0231-0.07440.43190.0114-0.06090.391-0.01040.3675-15.2674-37.216118.3072
120.0717-0.1484-0.09111.25511.41451.7813-0.1319-0.0062-0.06650.17510.09590.16320.27160.12740.14050.3755-0.00020.03090.42460.00890.4492-9.8604-50.338714.2662
132.32711.22850.47213.1927-0.13550.8751-0.23090.13280.2875-0.32350.23060.41070.04080.01330.02290.3771-0.0587-0.0470.3770.0760.3956-22.6717-50.78423.4835
141.8461-0.6034-0.49111.7997-1.72132.84620.00890.0864-0.1433-0.34840.29810.09620.1296-0.0368-0.28920.3917-0.03010.02460.3252-0.01980.3445-21.3389-65.33511.2884
152.90780.7050.3231.6561-0.21051.92060.1254-0.14670.6032-0.3712-0.0122-0.1478-0.32990.2148-0.17490.573-0.01950.04060.4223-0.05330.6049-8.4191-22.393-26.833
161.91380.7252-0.00712.5863-0.26952.79730.1549-0.52620.2120.2792-0.088-0.0271-0.24270.0918-0.04180.35130.0330.00990.4974-0.04940.3932-15.9961-33.493-17.0079
171.26560.1063-0.34851.3197-0.01251.6573-0.00850.09390.0011-0.022-0.00340.13990.0365-0.06250.03670.3205-0.0115-0.00460.3549-0.0020.3648-20.2972-42.783-30.5341
180.91820.69310.56471.7609-0.78341.6758-0.2749-0.53710.64170.36960.28260.01480.10190.12250.26960.4229-0.0144-0.02190.4391-0.04090.39827.0211-32.4018-50.5713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 16 )A3 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 57 )A17 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 143 )A58 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 198 )A144 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 216 )A199 - 216
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 35 )B3 - 35
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 57 )B36 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 130 )B58 - 130
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 195 )B131 - 195
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 216 )B196 - 216
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 16 )C3 - 16
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 57 )C17 - 57
13X-RAY DIFFRACTION13chain 'C' and (resid 58 through 156 )C58 - 156
14X-RAY DIFFRACTION14chain 'C' and (resid 157 through 215 )C157 - 215
15X-RAY DIFFRACTION15chain 'D' and (resid 3 through 57 )D3 - 57
16X-RAY DIFFRACTION16chain 'D' and (resid 58 through 136 )D58 - 136
17X-RAY DIFFRACTION17chain 'D' and (resid 137 through 195 )D137 - 195
18X-RAY DIFFRACTION18chain 'D' and (resid 196 through 216 )D196 - 216

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