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Open data
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Basic information
Entry | Database: PDB / ID: 3rod | ||||||
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Title | Methyltransferase | ||||||
![]() | Nicotinamide N-methyltransferase | ||||||
![]() | TRANSFERASE / METHYLTRANSFERASE | ||||||
Function / homology | ![]() pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, Y. / Yee, V.C. | ||||||
![]() | ![]() Title: Structural basis of substrate recognition in human nicotinamide N-methyltransferase. Authors: Peng, Y. / Sartini, D. / Pozzi, V. / Wilk, D. / Emanuelli, M. / Yee, V.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 | ![]() | 212.6 KB | Display | ![]() |
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PDB format | ![]() | 169.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 44.7 KB | Display | |
Data in CIF | ![]() | 58.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iipS S: Starting model for refinement |
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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: 31466.033 Da / Num. of mol.: 4 / Mutation: A100K, A101E, A103E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P40261, nicotinamide N-methyltransferase #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-NCA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.57 % |
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Crystal grow | Details: 25% PEG3350, 0.1 M BIS-TRIS; OR 25- 27% PEG3350, 0.2 M NACL, 0.1M BIS-TRIS OR IMIDAZOLE, PH 5.5 OR 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K PH range: 5.5 OR 6.5 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2008 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR. LN2 COOLED FIRST CRYSTAL, SAGITTAL FOCUSING 2ND CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→39.67 Å / Num. obs: 24960 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IIP Resolution: 2.72→39.67 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.72→39.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.79 Å / Total num. of bins used: 20
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