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- PDB-7vb8: SbSOMT in complex with resveratrol and nicotinamide adenine dinuc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vb8 | ||||||
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Title | SbSOMT in complex with resveratrol and nicotinamide adenine dinucleotide(NAD+) | ||||||
![]() | stilbene O-methyltransferase | ||||||
![]() | TRANSFERASE / resveratrol / 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 | ![]() | 182.4 KB | Display | ![]() |
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PDB format | ![]() | 139 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 | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 52.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7waqC ![]() 7warC ![]() 7wasC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 41533.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 597 molecules ![](data/chem/img/STL.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #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: 55.13 % |
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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: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→48.462 Å / Num. obs: 97225 / % possible obs: 99.8 % / Redundancy: 19.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4621 / CC1/2: 0.849 / Rpim(I) all: 0.357 / Rrim(I) all: 1.01 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MrBUMP generated chimeric model Resolution: 1.72→48.462 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.156 / SU B: 1.993 / SU ML: 0.063 / Average fsc free: 0.9712 / Average fsc work: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.089 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: 26.372 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→48.462 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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