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- PDB-5pa7: humanized rat COMT in complex with 6-bromo-3-chloroquinolin-8-ol -

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Basic information

Entry
Database: PDB / ID: 5pa7
Titlehumanized rat COMT in complex with 6-bromo-3-chloroquinolin-8-ol
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
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 / regulation of blood pressure / memory / response to wounding / cognition / response to estrogen / response to toxic substance / cell body / gene expression / methylation / vesicle / dendritic spine / response to oxidative stress / response to lipopolysaccharide / postsynaptic membrane / 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
6-bromanyl-3-chloranyl-quinolin-8-ol / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a COMT complex
Authors: Lerner, C. / Jakob-Roetne, R. / Groebke-Zbinden, K. / Buettelmann, B. / Rudolph, M.G.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Nov 17, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_deposit_group / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _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
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4868
Polymers49,3892
Non-polymers1,0986
Water1,63991
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3855
Polymers24,6941
Non-polymers6904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1023
Polymers24,6941
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.185, 60.105, 147.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catechol O-methyltransferase / Humanized rat COMT


Mass: 24694.332 Da / Num. of mol.: 2 / Fragment: SOLUBLE FORM, RESIDUES 44-264 / Mutation: M134I, Y138C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-7JX / 6-bromanyl-3-chloranyl-quinolin-8-ol


Mass: 258.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H5BrClNO
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
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 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.12→46.61 Å / Num. obs: 29641 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.61 % / Biso Wilson estimate: 39.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.151 / Rsym value: 0.124 / Χ2: 1.032 / Net I/σ(I): 8.36 / Num. measured all: 194595
Reflection shellResolution: 2.12→2.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.23 / Num. measured obs: 2234 / Num. possible: 408 / Num. unique obs: 401 / CC1/2: 0.999 / Rrim(I) all: 0.032 / Rsym value: 0.834 / Rejects: 0 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_764refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.12→45.204 Å / FOM work R set: 0.7879 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.15 / Stereochemistry target values: ML
Details: partial radiolysis of bromine. no sigma-hole effect of chlorine and amide carbonyl. lysine binds to said carbonyl.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1502 5.08 %random
Rwork0.1927 28063 --
obs0.1954 29565 99.72 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.927 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 141.96 Å2 / Biso mean: 49.72 Å2 / Biso min: 24.26 Å2
Baniso -1Baniso -2Baniso -3
1-21.6293 Å2-0 Å2-0 Å2
2---11.283 Å20 Å2
3----10.3463 Å2
Refinement stepCycle: final / Resolution: 2.12→45.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 68 91 3476
Biso mean--45.32 44.54 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073446
X-RAY DIFFRACTIONf_angle_d1.0674674
X-RAY DIFFRACTIONf_chiral_restr0.069531
X-RAY DIFFRACTIONf_plane_restr0.004593
X-RAY DIFFRACTIONf_dihedral_angle_d15.8131302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1201-2.18850.33871490.331424852634100
2.1885-2.26670.35911590.30352465262499
2.2667-2.35750.33571250.29042503262899
2.3575-2.46480.34291280.271125222650100
2.4648-2.59470.30551340.257525542688100
2.5947-2.75720.28091610.220324932654100
2.7572-2.97010.28841150.217625652680100
2.9701-3.26890.2871010.212125692670100
3.2689-3.74170.23561210.175525852706100
3.7417-4.71340.20251540.140525912745100
4.7134-45.21470.1911550.154827312886100
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)
11.9965-0.191-0.25763.93192.21363.6031-0.0839-0.2401-0.34890.27760.5247-0.08610.54230.851-0.38920.28430.04420.02280.4613-0.03510.342314.08-11.262521.8405
25.7305-1.6246-1.62924.97490.91485.16090.09250.32750.9566-0.20170.1983-0.8248-0.98840.4174-0.2420.4248-0.0531-0.00190.37860.02340.435212.7136-0.736218.7742
32.8844-1.297-0.3464.1259-0.22492.1689-0.0131-0.0772-0.1067-0.49960.04180.2047-0.42430.5394-0.03260.5086-0.03150.01730.46320.0610.39036.5826-0.29047.4578
41.00870.06560.80721.319-0.42940.97550.16730.32240.501-0.0966-0.296-0.0868-0.37060.19990.09660.35420.0701-0.01550.4116-0.01360.353-3.1472-5.383210.9645
50.95880.71920.17250.804-0.44451.3318-0.0005-0.13640.1192-0.05160.0351-0.0186-0.2005-0.0461-0.02130.3440.03250.00120.3368-0.02570.3388-1.5112-6.153917.5702
61.0817-0.36240.17562.7447-0.40880.8902-0.0177-0.1957-0.00620.2482-0.01810.3475-0.1434-0.32610.02650.2990.0471-0.04910.4844-0.0070.4283-15.357-11.262610.0358
72.66470.05090.19132.24660.58851.71730.02970.1565-0.1831-0.54790.1008-0.07950.4138-0.1275-0.13670.45110.0364-0.06320.32720.01360.2715-5.2557-12.07280.9101
81.55270.4046-0.13070.83130.45051.28-0.14970.17630.0461-0.55840.15670.2599-0.0166-0.15480.00270.51140.0152-0.0880.34810.0640.3419-4.7924-6.3117-4.2401
92.5481-0.8402-0.44551.8864-0.08491.0019-0.24750.23320.4815-0.61610.20090.0425-0.1469-0.2168-0.02830.6038-0.0036-0.02020.36510.06550.34783.7477-2.2715-3.3855
100.07380.0673-0.01140.09980.01580.0165-0.0926-0.17720.05940.1038-0.0577-0.101-0.09550.327700.53860.07630.13280.37790.05630.30611.9257-13.79178.9488
110.5548-0.1150.07220.2907-0.13210.0611-0.17550.0444-0.0907-0.0288-0.2264-0.19840.09210.0729-0.00910.41090.02150.12691.0326-0.18730.56258.7554-11.83153.4989
122.05711.2727-0.27031.078-0.49734.03350.03070.45091.18630.03960.5880.7927-0.869-0.5398-0.21380.3690.3326-0.01850.70660.13660.7242-23.0059-20.57529.299
133.60760.62510.63431.5666-1.13351.17670.1713-0.22950.1909-0.0929-0.2810.516-0.1189-0.3432-0.0070.46050.05550.05610.46920.03050.3761-8.1258-25.165420.8891
141.4546-1.0414-0.03621.454-1.08172.8722-0.07390.05320.0059-0.37530.13510.45990.4137-0.5802-0.07750.333-0.0818-0.07530.36280.00120.4166-14.1408-37.72829.1447
150.87780.9981-0.16581.4144-0.53511.7971-0.05840.0299-0.1221-0.0715-0.0919-0.15960.12040.11790.14950.2930.06190.01440.2779-0.00450.30052.6139-33.0828.5592
160.02640.0089-0.02320.0372-0.02420.0340.05640.2040.2594-0.0285-0.00730.19750.0232-0.1469-0.00010.46950.03420.09540.44370.06120.4815-10.2707-31.31136.5609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:16)A3 - 16
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:35)A17 - 35
3X-RAY DIFFRACTION3chain 'A' and (resseq 36:57)A36 - 57
4X-RAY DIFFRACTION4chain 'A' and (resseq 58:70)A58 - 70
5X-RAY DIFFRACTION5chain 'A' and (resseq 71:118)A71 - 118
6X-RAY DIFFRACTION6chain 'A' and (resseq 119:136)A119 - 136
7X-RAY DIFFRACTION7chain 'A' and (resseq 137:156)A137 - 156
8X-RAY DIFFRACTION8chain 'A' and (resseq 157:188)A157 - 188
9X-RAY DIFFRACTION9chain 'A' and (resseq 189:215)A189 - 215
10X-RAY DIFFRACTION10chain 'A' and (resseq 300:300)A300
11X-RAY DIFFRACTION11chain 'A' and (resseq 301:302)A301 - 302
12X-RAY DIFFRACTION12chain 'B' and (resseq 3:35)B3 - 35
13X-RAY DIFFRACTION13chain 'B' and (resseq 36:57)B36 - 57
14X-RAY DIFFRACTION14chain 'B' and (resseq 58:143)B58 - 143
15X-RAY DIFFRACTION15chain 'B' and (resseq 144:216)B144 - 216
16X-RAY DIFFRACTION16chain 'B' and (resseq 300:300)B300

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