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- PDB-6i3d: Crystal structure of Human soluble catechol O-methyltransferase i... -

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Basic information

Entry
Database: PDB / ID: 6i3d
TitleCrystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and Sinefungin
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / Enzyme / S-adenosyl-L-methionine / Catechol O-methyltransferase
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 / 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 / renal sodium excretion / : / : / renin secretion into blood stream / developmental process / catechol O-methyltransferase / renal filtration / renal albumin absorption / dopamine secretion / Methylation / habituation / artery development / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / synaptic transmission, dopaminergic / O-methyltransferase activity / cholesterol efflux / response to angiotensin / cellular response to cocaine / exploration behavior / response to food / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / response to amphetamine / response to cytokine / methyltransferase activity / multicellular organism growth / visual learning / memory / response to toxic substance / response to wounding / gene expression / methylation / response to oxidative stress / 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 / 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
3,5-DINITROCATECHOL / SINEFUNGIN / Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European CommissionPITN-GA-2013-ITN 606831 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase.
Authors: Czarnota, S. / Johannissen, L.O. / Baxter, N.J. / Rummel, F. / Wilson, A.L. / Cliff, M.J. / Levy, C.W. / Scrutton, N.S. / Waltho, J.P. / Hay, S.
History
DepositionNov 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release

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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)53,1538
Polymers51,9412
Non-polymers1,2126
Water7,584421
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5764
Polymers25,9711
Non-polymers6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5764
Polymers25,9711
Non-polymers6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.961, 75.797, 64.345
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25970.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMT / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P21964, catechol O-methyltransferase
#2: Chemical ChemComp-DNC / 3,5-DINITROCATECHOL


Mass: 200.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M amino acid stock (0.2M L-Na-Glutamate; 0.2M Alananine (racemic); 0.2M Glycine; 0.2M Lysine HCL (racemic); 0.2M Serine (racemic), 0.1M Imidazole; MES monohydrate (acid) pH 6.5, 50% v/v ...Details: 0.1M amino acid stock (0.2M L-Na-Glutamate; 0.2M Alananine (racemic); 0.2M Glycine; 0.2M Lysine HCL (racemic); 0.2M Serine (racemic), 0.1M Imidazole; MES monohydrate (acid) pH 6.5, 50% v/v precipitant mix (25% v/v MPD; 25% PEG 1000; 25% PEG 3350) Morpheus condition H4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→37.02 Å / Num. obs: 72308 / % possible obs: 99.38 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 15.5
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.32 / Num. unique obs: 7205 / CC1/2: 0.98 / Rpim(I) all: 0.17 / Rrim(I) all: 0.31 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX(dev_3304: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse

Resolution: 1.45→37.02 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.15
RfactorNum. reflection% reflection
Rfree0.146 3514 4.86 %
Rwork0.1188 --
obs0.1202 72301 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 84 421 3886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013843
X-RAY DIFFRACTIONf_angle_d1.1145259
X-RAY DIFFRACTIONf_dihedral_angle_d2.7972524
X-RAY DIFFRACTIONf_chiral_restr0.09582
X-RAY DIFFRACTIONf_plane_restr0.007690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46990.231390.15612732X-RAY DIFFRACTION100
1.4699-1.49090.16781280.13272783X-RAY DIFFRACTION100
1.4909-1.51310.17551310.10922727X-RAY DIFFRACTION100
1.5131-1.53680.14891460.10272781X-RAY DIFFRACTION100
1.5368-1.5620.14291300.0992743X-RAY DIFFRACTION100
1.562-1.58890.1481430.09672787X-RAY DIFFRACTION100
1.5889-1.61780.16061600.09962712X-RAY DIFFRACTION100
1.6178-1.64890.13531670.09562756X-RAY DIFFRACTION100
1.6489-1.68260.13971500.09472712X-RAY DIFFRACTION100
1.6826-1.71920.16081570.09662780X-RAY DIFFRACTION100
1.7192-1.75920.16141580.12701X-RAY DIFFRACTION100
1.7592-1.80320.1591520.1042768X-RAY DIFFRACTION100
1.8032-1.85190.13671250.10152775X-RAY DIFFRACTION100
1.8519-1.90640.15441330.10072746X-RAY DIFFRACTION99
1.9064-1.9680.14921360.10542763X-RAY DIFFRACTION100
1.968-2.03830.14231380.10992769X-RAY DIFFRACTION100
2.0383-2.11990.15761210.11192762X-RAY DIFFRACTION100
2.1199-2.21640.14161260.11272754X-RAY DIFFRACTION99
2.2164-2.33320.14041260.11552747X-RAY DIFFRACTION99
2.3332-2.47940.1361540.11372753X-RAY DIFFRACTION99
2.4794-2.67080.15741200.12852766X-RAY DIFFRACTION99
2.6708-2.93960.1381170.13552746X-RAY DIFFRACTION98
2.9396-3.36490.14791550.13392722X-RAY DIFFRACTION98
3.3649-4.2390.13971400.11662741X-RAY DIFFRACTION98
4.239-48.98830.13531620.14482761X-RAY DIFFRACTION98

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