+Open data
-Basic information
Entry | Database: PDB / ID: 3rod | ||||||
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Title | Methyltransferase | ||||||
Components | Nicotinamide N-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information 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 / response to organonitrogen compound / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Peng, Y. / Yee, V.C. | ||||||
Citation | Journal: Biochemistry / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rod.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rod.ent.gz | 169.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/3rod ftp://data.pdbj.org/pub/pdb/validation_reports/ro/3rod | HTTPS FTP |
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-Related structure data
Related structure data | 2iipS S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: NNMT / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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