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- PDB-5zy6: catechol methyltransferase spCOMT -

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Basic information

Entry
Database: PDB / ID: 5zy6
Titlecatechol methyltransferase spCOMT
ComponentsProbable catechol O-methyltransferase 1
KeywordsTRANSFERASE / catechol / methyltransferase
Function / homology
Function and homology information


Methylation / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / carboxyl-O-methyltransferase activity / catechol O-methyltransferase / catecholamine metabolic process / O-methyltransferase activity / cellular detoxification / methylation / metal ion binding ...Methylation / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / carboxyl-O-methyltransferase activity / catechol O-methyltransferase / catecholamine metabolic process / O-methyltransferase activity / cellular detoxification / methylation / metal ion binding / nucleus / cytosol
Similarity search - Function
Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Probable catechol O-methyltransferase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsWang, Q. / Xu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1732114, 31770788, 31770895 China
CitationJournal: To Be Published
Title: structural insight into spCOMT
Authors: Wang, Q.
History
DepositionMay 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable catechol O-methyltransferase 1
B: Probable catechol O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6234
Polymers62,8262
Non-polymers7972
Water5,477304
1
A: Probable catechol O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8112
Polymers31,4131
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable catechol O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8112
Polymers31,4131
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.265, 78.858, 102.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable catechol O-methyltransferase 1


Mass: 31413.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O42898, catechol O-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 21% PEG4000, 0.1% MES pH5.6, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 34385 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 35
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 9 / Num. unique obs: 1668 / Rsym value: 0.253 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pyj

4pyj


Resolution: 2.099→36.813 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2342 1733 5.05 %
Rwork0.1854 --
obs0.1879 34326 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.099→36.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 54 304 4226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084002
X-RAY DIFFRACTIONf_angle_d1.095410
X-RAY DIFFRACTIONf_dihedral_angle_d13.241511
X-RAY DIFFRACTIONf_chiral_restr0.047595
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0991-2.16090.27561310.20752665X-RAY DIFFRACTION99
2.1609-2.23060.26421310.18122693X-RAY DIFFRACTION99
2.2306-2.31030.28611250.18872707X-RAY DIFFRACTION99
2.3103-2.40280.27271530.19412632X-RAY DIFFRACTION99
2.4028-2.51220.24961330.192703X-RAY DIFFRACTION99
2.5122-2.64460.26511280.20092710X-RAY DIFFRACTION100
2.6446-2.81020.24661530.20072691X-RAY DIFFRACTION100
2.8102-3.02710.23971490.20152709X-RAY DIFFRACTION100
3.0271-3.33150.25371430.20712715X-RAY DIFFRACTION99
3.3315-3.81320.25991490.17612742X-RAY DIFFRACTION100
3.8132-4.80250.18971800.15212758X-RAY DIFFRACTION100
4.8025-36.81880.19351580.18392868X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.5584 Å / Origin y: 9.2522 Å / Origin z: -6.8336 Å
111213212223313233
T0.1473 Å20.0249 Å2-0.0322 Å2-0.1631 Å2-0.0014 Å2--0.1688 Å2
L-0.0273 °2-0.2192 °2-0.1687 °2-0.8689 °20.5691 °2--0.2897 °2
S-0.0256 Å °0.0137 Å °-0.0072 Å °-0.0585 Å °-0.0122 Å °0.0613 Å °-0.0668 Å °-0.0382 Å °0.0256 Å °
Refinement TLS groupSelection details: all

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