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- PDB-8j3g: Crystal structure of apo (S)-norcoclaurine 6-O-methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 8j3g
TitleCrystal structure of apo (S)-norcoclaurine 6-O-methyltransferase from Coptis chinensis
Components6-O-methyltransferase 2 (Fragment)
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
6-O-methyltransferase 2
Similarity search - Component
Biological speciesCoptis chinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, X.H. / Su, D. / Zhang, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0505903 China
CitationJournal: To Be Published
Title: Crystal structure of apo (S)-norcoclaurine 6-O-methyltransferase from Coptis chinensis
Authors: Li, X.H. / Su, D. / Zhang, C.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: 6-O-methyltransferase 2 (Fragment)


Theoretical massNumber of molelcules
Total (without water)38,7731
Polymers38,7731
Non-polymers00
Water1,58588
1
A: 6-O-methyltransferase 2 (Fragment)

A: 6-O-methyltransferase 2 (Fragment)


Theoretical massNumber of molelcules
Total (without water)77,5462
Polymers77,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area8130 Å2
ΔGint-65 kcal/mol
Surface area28240 Å2
MethodPISA
2
A: 6-O-methyltransferase 2 (Fragment)

A: 6-O-methyltransferase 2 (Fragment)


Theoretical massNumber of molelcules
Total (without water)77,5462
Polymers77,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.479, 103.935, 101.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

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Components

#1: Protein 6-O-methyltransferase 2 (Fragment)


Mass: 38772.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptis chinensis (plant) / Gene: 6OMT2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5FRS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES (pH=6.0), 8% PEG400, 0.05 M sodium fluoride

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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: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18402 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 4.3
Reflection shellResolution: 2.3→2.3 Å / Num. unique obs: 891 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.98 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 915 5.01 %
Rwork0.1928 --
obs0.1947 18255 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 88 2532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062558
X-RAY DIFFRACTIONf_angle_d0.8793454
X-RAY DIFFRACTIONf_dihedral_angle_d5.832337
X-RAY DIFFRACTIONf_chiral_restr0.052394
X-RAY DIFFRACTIONf_plane_restr0.007434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30031150.20822418X-RAY DIFFRACTION98
2.42-2.570.24211450.20912431X-RAY DIFFRACTION99
2.57-2.770.27541180.2182434X-RAY DIFFRACTION99
2.77-3.040.27421360.22952475X-RAY DIFFRACTION100
3.04-3.480.28361300.22262480X-RAY DIFFRACTION100
3.48-4.380.21831230.17932516X-RAY DIFFRACTION100
4.39-25.980.18611480.1682586X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 49.3559 Å / Origin y: 13.2322 Å / Origin z: 62.6398 Å
111213212223313233
T0.3698 Å20.0102 Å2-0.016 Å2-0.2935 Å2-0.0047 Å2--0.3312 Å2
L0.9481 °2-0.1384 °2-0.4146 °2-0.4357 °20.0661 °2--0.9974 °2
S0.0222 Å °0.061 Å °-0.0294 Å °-0.0837 Å °0.0094 Å °-0.0227 Å °0.1133 Å °0.0983 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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