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- PDB-7was: SbSOMT in complex with pterostilbene and nicotinamide adenine din... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7was | ||||||
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Title | SbSOMT in complex with pterostilbene and nicotinamide adenine dinucleotide(NAD+) | ||||||
![]() | stilbene O-methyltransferase | ||||||
![]() | TRANSFERASE / pterostilbene / complex / o-methyltransferase / substrate | ||||||
Function / homology | ![]() : / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pow, K.C. / Hao, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regioselective stilbene O-methylations in Saccharinae grasses. Authors: Lui, A.C.W. / Pow, K.C. / Lin, N. / Lam, L.P.Y. / Liu, G. / Godwin, I.D. / Fan, Z. / Khoo, C.J. / Tobimatsu, Y. / Wang, L. / Hao, Q. / Lo, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171 KB | Display | ![]() |
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PDB format | ![]() | 129.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vb8SC ![]() 7waqC ![]() 7warC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 15 - 377 / Label seq-ID: 14 - 376
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41402.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 188 molecules ![](data/chem/img/3RL.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6, 0.2 M sodium acetate , 0.2 M ammonium chloride, 2.5% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.401→31.421 Å / Num. obs: 36363 / % possible obs: 99.8 % / Redundancy: 19.5 % / Biso Wilson estimate: 36.78 Å2 / CC1/2: 0.915 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.046 / Rrim(I) all: 0.204 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.401→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1774 / CC1/2: 0.871 / Rpim(I) all: 0.228 / Rrim(I) all: 0.982 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7vb8 Resolution: 2.401→31.421 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.181 / SU B: 6.812 / SU ML: 0.163 / Average fsc free: 0.9597 / Average fsc work: 0.9768 / Cross valid method: FREE R-VALUE / ESU R: 0.364 / ESU R Free: 0.255 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.738 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→31.421 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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