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- PDB-5fhr: Crystal structure of Y200L mutant of Rat Catechol-O-Methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 5fhr
TitleCrystal structure of Y200L mutant of Rat Catechol-O-Methyltransferase in complex with AdoMet and 3,5-dinitrocatechol
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Methyltransferase Regioselectivity
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 / catechol-containing compound metabolic process / catecholamine catabolic 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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / negative regulation of dopamine metabolic process / renal albumin absorption / catecholamine metabolic process / habituation / artery development / response to salt / short-term memory / S-adenosylmethionine metabolic process / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / 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 / prostaglandin metabolic process / glycogen metabolic process / dopamine 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 / response to cytokine / kidney development / 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 / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / response to oxidative stress / 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
BROMIDE ION / 3,5-DINITROCATECHOL / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsLevy, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase.
Authors: Law, B.J. / Bennett, M.R. / Thompson, M.L. / Levy, C. / Shepherd, S.A. / Leys, D. / Micklefield, J.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 10, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1899
Polymers47,8632
Non-polymers1,3267
Water13,133729
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-44 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.700, 79.370, 109.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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


Mass: 23931.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 5 types, 736 molecules

#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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200nl of protein mixed with an equal volume of 0.09 M [0.3 M sodium fluoride; 0.3 M sodium bromide; 0.3 M sodium iodide], 0.1 M Tris / Bicine pH 8.5, 50% [40% v/v PEG 500* MME; 20 % w/v PEG ...Details: 200nl of protein mixed with an equal volume of 0.09 M [0.3 M sodium fluoride; 0.3 M sodium bromide; 0.3 M sodium iodide], 0.1 M Tris / Bicine pH 8.5, 50% [40% v/v PEG 500* MME; 20 % w/v PEG 20000] Morpheus HT96 condition B9
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.63→48.713 Å / Num. obs: 66577 / % possible obs: 98 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.63
Reflection shellResolution: 1.63→1.68 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.98 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NWE

3nwe


Resolution: 1.63→48.713 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 3377 5.07 %Random selection
Rwork0.1589 ---
obs0.1599 66571 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→48.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 85 729 4164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013504
X-RAY DIFFRACTIONf_angle_d1.3374758
X-RAY DIFFRACTIONf_dihedral_angle_d13.3141294
X-RAY DIFFRACTIONf_chiral_restr0.079538
X-RAY DIFFRACTIONf_plane_restr0.007605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65330.23751630.20552566X-RAY DIFFRACTION98
1.6533-1.6780.26481530.20092573X-RAY DIFFRACTION98
1.678-1.70420.25321530.19462608X-RAY DIFFRACTION98
1.7042-1.73210.24111320.1962591X-RAY DIFFRACTION98
1.7321-1.7620.23631380.1932631X-RAY DIFFRACTION98
1.762-1.7940.2141300.18662609X-RAY DIFFRACTION99
1.794-1.82850.21981380.18092619X-RAY DIFFRACTION99
1.8285-1.86590.21331390.1752613X-RAY DIFFRACTION99
1.8659-1.90640.18611370.15692629X-RAY DIFFRACTION99
1.9064-1.95080.19211350.15922607X-RAY DIFFRACTION99
1.9508-1.99960.17481290.15412670X-RAY DIFFRACTION99
1.9996-2.05360.18531240.15352667X-RAY DIFFRACTION99
2.0536-2.11410.17541300.15272627X-RAY DIFFRACTION99
2.1141-2.18230.1631330.14972376X-RAY DIFFRACTION89
2.1823-2.26030.16911370.15032644X-RAY DIFFRACTION99
2.2603-2.35080.18751450.14742639X-RAY DIFFRACTION99
2.3508-2.45780.15841400.15172681X-RAY DIFFRACTION99
2.4578-2.58740.17521380.15182680X-RAY DIFFRACTION99
2.5874-2.74950.16071500.15372669X-RAY DIFFRACTION99
2.7495-2.96170.17771430.16642700X-RAY DIFFRACTION100
2.9617-3.25970.1921410.16232698X-RAY DIFFRACTION99
3.2597-3.73130.14861470.15112686X-RAY DIFFRACTION99
3.7313-4.70040.12981400.12922539X-RAY DIFFRACTION92
4.7004-48.73440.18371620.16912872X-RAY DIFFRACTION99

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