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- PDB-8j3i: Crystal structure of (S)-scoulerine 9-O-methyltransferase from Co... -

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Basic information

Entry
Database: PDB / ID: 8j3i
TitleCrystal structure of (S)-scoulerine 9-O-methyltransferase from Coptis chinensis
Components(S)-scoulerine 9-O-methyltransferase
KeywordsBIOSYNTHETIC PROTEIN / homodimers
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
(S)-scoulerine 9-O-methyltransferase
Similarity search - Component
Biological speciesCoptis chinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLi, X.H. / Su, D. / Lei, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0505903 China
CitationJournal: To Be Published
Title: Crystal structure of (S)-scoulerine 9-O-methyltransferase from Coptis chinensis
Authors: Li, X.H. / Su, D. / Lei, J.H.
History
DepositionApr 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-scoulerine 9-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)38,3291
Polymers38,3291
Non-polymers00
Water181
1
A: (S)-scoulerine 9-O-methyltransferase

A: (S)-scoulerine 9-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)76,6582
Polymers76,6582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8370 Å2
ΔGint-74 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.467, 99.467, 99.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein (S)-scoulerine 9-O-methyltransferase


Mass: 38328.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptis chinensis (plant) / Gene: IFM89_036405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A835IHU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH8.5, 1.7 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.39→19.86 Å / Num. obs: 22428 / % possible obs: 98.74 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 3.5
Reflection shellResolution: 2.39→2.54 Å / Num. unique obs: 3294 / CC1/2: 0.13

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→19.86 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 1989 8.87 %
Rwork0.2253 --
obs0.2302 22426 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 1 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.055
X-RAY DIFFRACTIONf_dihedral_angle_d16.847987
X-RAY DIFFRACTIONf_chiral_restr0.062416
X-RAY DIFFRACTIONf_plane_restr0.008476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.50731330.48421344X-RAY DIFFRACTION92
2.45-2.520.46021410.39271420X-RAY DIFFRACTION98
2.52-2.590.44671390.37451440X-RAY DIFFRACTION99
2.59-2.680.34021410.33071474X-RAY DIFFRACTION99
2.68-2.770.38451380.32261423X-RAY DIFFRACTION99
2.77-2.880.35291380.31191444X-RAY DIFFRACTION98
2.88-3.010.36721450.32091450X-RAY DIFFRACTION99
3.01-3.170.36821360.27031442X-RAY DIFFRACTION99
3.17-3.370.35671460.29431462X-RAY DIFFRACTION99
3.37-3.630.3671430.25591465X-RAY DIFFRACTION100
3.63-3.990.26841470.22111494X-RAY DIFFRACTION100
3.99-4.560.20661420.18171486X-RAY DIFFRACTION100
4.56-5.720.2331510.19351507X-RAY DIFFRACTION100
5.73-6.540.2161490.15771586X-RAY DIFFRACTION100

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