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- PDB-5kok: Pavine N-methyltransferase in complex with Tetrahydropapaverine a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kok | ||||||
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Title | Pavine N-methyltransferase in complex with Tetrahydropapaverine and S-adenosylhomocysteine pH 7.25 | ||||||
![]() | Pavine N-methyltransferase | ||||||
![]() | TRANSFERASE / benzylisoquinoline alkaloid biosynthesis | ||||||
Function / homology | ![]() pavine N-methyltransferase / methyltransferase activity / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torres, M.A. / Hoffarth, E. / Eugenio, L. / Savtchouk, J. / Chen, X. / Morris, J. / Facchini, P.J. / Ng, K.K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional Studies of Pavine N-Methyltransferase from Thalictrum flavum Reveal Novel Insights into Substrate Recognition and Catalytic Mechanism. Authors: Torres, M.A. / Hoffarth, E. / Eugenio, L. / Savtchouk, J. / Chen, X. / Morris, J.S. / Facchini, P.J. / Ng, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | 134.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kn4SC ![]() 5kocC ![]() 5kpcC ![]() 5kpgC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46436.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pRSETC / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.91 % / Description: Plate-like, 0.2x0.2 mm |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 210 g/L polyethylene glycol 3350, 100 mM sodium HEPES pH 7.25, 75 mM potassium chloride, 120 g/L glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.792→39.297 Å / Num. obs: 65359 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.169 / Rsym value: 0.169 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.792→1.8179 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 7.57 / CC1/2: 0.982 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KN4 Resolution: 1.792→39.297 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→39.297 Å
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Refine LS restraints |
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LS refinement shell |
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