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Yorodumi- PDB-6p3m: Tetrahydroprotoberberine N-methyltransferase in complex with S-ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p3m | ||||||
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Title | Tetrahydroprotoberberine N-methyltransferase in complex with S-adenosylhomocysteine | ||||||
Components | tetrahydroprotoberberine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | ||||||
Biological species | Glaucium flavum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lang, D.E. / Morris, J.S. / Rowley, M. / Torres, M.A. / Maksimovich, V.A. / Facchini, P.J. / Ng, K.K.S. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structure-function studies of tetrahydroprotoberberineN-methyltransferase reveal the molecular basis of stereoselective substrate recognition. Authors: Lang, D.E. / Morris, J.S. / Rowley, M. / Torres, M.A. / Maksimovich, V.A. / Facchini, P.J. / Ng, K.K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p3m.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p3m.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p3m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6p3m_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6p3m_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 6p3m_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/6p3m ftp://data.pdbj.org/pub/pdb/validation_reports/p3/6p3m | HTTPS FTP |
-Related structure data
Related structure data | 6p3nC 6p3oC 5kokS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 43801.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glaucium flavum (plant) / Production host: Escherichia coli (E. coli) / References: EC: 2.1.1.122 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium Sulfate, Glycerol, Pentaerythritol ethoxylate (15/4 EO/OH), Tris-Cl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.6 Å / Num. obs: 48045 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 1 / Rrim(I) all: 0.056 / Rsym value: 0.055 / Net I/σ(I): 26.93 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 3522 / CC1/2: 0.773 / Rrim(I) all: 1.17 / Rsym value: 1.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KOK Resolution: 1.8→37.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.89 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.506 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→37.6 Å
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Refine LS restraints |
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