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Yorodumi- PDB-6nej: scoulerine 9-O-methyltransferase from Thalictrum flavum complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nej | ||||||
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Title | scoulerine 9-O-methyltransferase from Thalictrum flavum complexed (13aS)-3,10-dimethoxy-5,8,13,13a-tetrahydro-6H-isoquino[3,2-a]isoquinoline-2,9-diol and with S-ADENOSYL-L-HOMOCYSTEINE | ||||||
Components | (S)-scoulerine 9-O-methyltransferase(S)-scoulerine 9-O-methyltransferase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Scoulerine / Methyltransferase / Benzylisoquinoline Alkaloid / Plant natural products | ||||||
Function / homology | Function and homology information (S)-scoulerine 9-O-methyltransferase / (S)-scoulerine 9-O-methyltransferase activity / : / O-methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Thalictrum flavum subsp. glaucum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Valentic, T.R. / Smolke, C.D. / Payne, J.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural and functional characterization of the scoulerine 9-O methyltransferase from Thalictrum flavum. Authors: Valentic, T.R. / Smolke, C.S. / Payne, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nej.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nej.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/6nej ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6nej | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40798.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant) Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5C9L2, (S)-scoulerine 9-O-methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.49 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350 and 0.22M AmSO4 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 106 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127085 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.72 Å / Num. obs: 74066 / % possible obs: 97.5 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.034 / Rrim(I) all: 0.102 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3634 / CC1/2: 0.896 / Rpim(I) all: 0.322 / Rrim(I) all: 0.953 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Thalictrum Flavum scoulerine 9-O-methyltranserase N191D F205S Resolution: 1.6→47.159 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.159 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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