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- PDB-8xe2: O-methyltransferase from Lycoris longituba D230A variant complexe... -

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Basic information

Entry
Database: PDB / ID: 8xe2
TitleO-methyltransferase from Lycoris longituba D230A variant complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde
Componentsnorbelladine O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase family protein / LlOMT
Function / homology
Function and homology information


norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
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
Protocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE / norbelladine O-methyltransferase
Similarity search - Component
Biological speciesLycoris longituba (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSaw, Y.Y.H. / Nakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H02777 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15303 Japan
CitationJournal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.
History
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: norbelladine O-methyltransferase
B: norbelladine O-methyltransferase
C: norbelladine O-methyltransferase
D: norbelladine O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69316
Polymers109,5974
Non-polymers2,09512
Water3,729207
1
A: norbelladine O-methyltransferase
hetero molecules

C: norbelladine O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9389
Polymers54,7992
Non-polymers1,1407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area4670 Å2
ΔGint-35 kcal/mol
Surface area18200 Å2
MethodPISA
2
D: norbelladine O-methyltransferase
hetero molecules

B: norbelladine O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7547
Polymers54,7992
Non-polymers9565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area4180 Å2
ΔGint-35 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.514, 81.596, 116.427
Angle α, β, γ (deg.)90.000, 91.372, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
norbelladine O-methyltransferase


Mass: 27399.338 Da / Num. of mol.: 4 / Mutation: D230A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycoris longituba (plant) / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A6B9TNK2

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Non-polymers , 5 types, 219 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-H6N / Protocatechuic aldehyde


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 11% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.048 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.048 Å / Relative weight: 1
ReflectionResolution: 2.43→47.38 Å / Num. obs: 67489 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.7
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3709 / CC1/2: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→47.38 Å / Cross valid method: FREE R-VALUE / σ(F): 2.31 / Phase error: 29.2486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 3593 5.32 %
Rwork0.2074 63896 -
obs0.2138 67489 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.75 Å2
Refinement stepCycle: LAST / Resolution: 2.43→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7675 0 12 207 7894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217970
X-RAY DIFFRACTIONf_angle_d0.550910838
X-RAY DIFFRACTIONf_chiral_restr0.04231218
X-RAY DIFFRACTIONf_plane_restr0.00391388
X-RAY DIFFRACTIONf_dihedral_angle_d17.74311126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.470.31691890.30523313X-RAY DIFFRACTION94.01
2.47-2.530.36992160.2953132X-RAY DIFFRACTION93.02
2.53-2.580.29871750.29533276X-RAY DIFFRACTION94.22
2.58-2.640.33921520.28583252X-RAY DIFFRACTION94.78
2.64-2.70.37131380.27123215X-RAY DIFFRACTION95.15
2.7-2.770.31611600.27273285X-RAY DIFFRACTION94.53
2.77-2.840.28361640.26853205X-RAY DIFFRACTION94.4
2.84-2.920.27591880.26953188X-RAY DIFFRACTION93.57
2.92-3.010.30821880.25483232X-RAY DIFFRACTION93.36
3.01-3.110.29771710.24283196X-RAY DIFFRACTION93.92
3.11-3.230.28691610.23063185X-RAY DIFFRACTION93.76
3.23-3.370.24512190.21833181X-RAY DIFFRACTION90.6
3.37-3.550.25151510.20592926X-RAY DIFFRACTION87.34
3.55-3.790.22481520.20313148X-RAY DIFFRACTION91.75
3.79-4.060.22731680.19593218X-RAY DIFFRACTION93.52
4.06-4.40.21661990.17853181X-RAY DIFFRACTION92.55
4.4-4.830.20671620.16553204X-RAY DIFFRACTION93.63
4.83-5.420.20391290.16893189X-RAY DIFFRACTION94.24
5.42-6.410.19231930.20263176X-RAY DIFFRACTION92.76
6.41-47.380.20162030.17563185X-RAY DIFFRACTION92.11

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