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- PDB-8zn0: The Crystal Structure of an Atypical N-methyltransferasea PaOMT9 ... -

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Basic information

Entry
Database: PDB / ID: 8zn0
TitleThe Crystal Structure of an Atypical N-methyltransferasea PaOMT9 in P. amurense
ComponentsPaOMT9
KeywordsTRANSFERASE / N-methyltransferasea PaOMT9
Function / homology: / S-ADENOSYLMETHIONINE
Function and homology information
Biological speciesPhellodendron amurense (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, Z.C. / Tian, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a N-methylated OMT from P. amurense in complex with SAM and (S)-coclaurine
Authors: Xu, Z.C. / Tian, Y.
History
DepositionMay 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaOMT9
B: PaOMT9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5086
Polymers80,1402
Non-polymers1,3684
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-72 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.346, 66.346, 167.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein PaOMT9


Mass: 40070.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phellodendron amurense (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1D8J / (1~{S})-1-[(4-hydroxyphenyl)methyl]-6-methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol / Coclaurine


Mass: 285.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG1000, 100 mM lithium sulfate monohydrate and 100 mM sodium citrate tribasic dihydrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→46.91 Å / Num. obs: 66419 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.327 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3846 / CC1/2: 0.626 / Rpim(I) all: 0.573 / Rrim(I) all: 1.429 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.91 Å / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 41.1391 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2044 3243 4.89 %
Rwork0.161 63108 -
obs0.2167 66351 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 96 134 5594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01135595
X-RAY DIFFRACTIONf_angle_d0.90147614
X-RAY DIFFRACTIONf_chiral_restr0.3426874
X-RAY DIFFRACTIONf_plane_restr0.0057965
X-RAY DIFFRACTIONf_dihedral_angle_d17.90051978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.35691540.31063094X-RAY DIFFRACTION94.42
1.83-1.870.37241500.31553126X-RAY DIFFRACTION95.42
1.87-1.90.30611690.31663170X-RAY DIFFRACTION94.91
1.9-1.940.33041800.31253139X-RAY DIFFRACTION94.58
1.94-1.980.3581710.31943102X-RAY DIFFRACTION94.78
1.98-2.030.35111560.31813206X-RAY DIFFRACTION95.33
2.03-2.080.39461560.32453146X-RAY DIFFRACTION95.28
2.08-2.140.38291780.31653152X-RAY DIFFRACTION94.65
2.14-2.20.39611530.31033136X-RAY DIFFRACTION95.35
2.2-2.270.37731720.31143126X-RAY DIFFRACTION94.78
2.27-2.350.34761390.29343215X-RAY DIFFRACTION95.86
2.35-2.450.3431510.28313139X-RAY DIFFRACTION95.41
2.45-2.560.37441620.27453181X-RAY DIFFRACTION95.15
2.56-2.690.30721420.26293161X-RAY DIFFRACTION95.7
2.69-2.860.28021730.24383159X-RAY DIFFRACTION94.81
2.86-3.080.21671810.21223115X-RAY DIFFRACTION94.48
3.08-3.390.24371490.17953173X-RAY DIFFRACTION95.51
3.39-3.880.20211670.13953164X-RAY DIFFRACTION94.99
3.88-4.880.14631560.10173188X-RAY DIFFRACTION95.31
4.88-23.980.17041840.12663175X-RAY DIFFRACTION94.52

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