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- PDB-5zy5: spCOMT apo structure -

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Basic information

Entry
Database: PDB / ID: 5zy5
TitlespCOMT apo structure
ComponentsProbable catechol O-methyltransferase 1
KeywordsTRANSFERASE / catechol-O-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
Probable catechol O-methyltransferase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsWang, Q. / Xu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1732114, 31770788 and 31770895 China
CitationJournal: To Be Published
Title: structural and functional investigations of spCOMT
Authors: Wang, Q. / Li, X.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,8262
Polymers62,8262
Non-polymers00
Water2,720151
1
A: Probable catechol O-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)31,4131
Polymers31,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable catechol O-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)31,4131
Polymers31,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.420, 79.792, 104.519
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 (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPBC119.03 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O42898, catechol O-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 4000, 0.1M MES pH5.6, 0.15M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 27483 / % possible obs: 94.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.68
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.371 / Num. unique obs: 2744 / Rsym value: 0.371

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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: 2.295→35.055 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2461 1332 5 %
Rwork0.1937 --
obs0.1962 26639 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→35.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 0 151 3920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083840
X-RAY DIFFRACTIONf_angle_d1.0935191
X-RAY DIFFRACTIONf_dihedral_angle_d12.0051425
X-RAY DIFFRACTIONf_chiral_restr0.044581
X-RAY DIFFRACTIONf_plane_restr0.006667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2951-2.37720.29981130.19932230X-RAY DIFFRACTION84
2.3772-2.47230.27561340.20122378X-RAY DIFFRACTION91
2.4723-2.58480.27791250.20572492X-RAY DIFFRACTION94
2.5848-2.7210.26941360.20992549X-RAY DIFFRACTION97
2.721-2.89140.26691270.21032602X-RAY DIFFRACTION99
2.8914-3.11450.29441450.22242612X-RAY DIFFRACTION99
3.1145-3.42770.22831310.20222617X-RAY DIFFRACTION98
3.4277-3.92320.24091470.19032594X-RAY DIFFRACTION97
3.9232-4.94060.20471530.16182610X-RAY DIFFRACTION96
4.9406-35.05890.24031210.18982623X-RAY DIFFRACTION92

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