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Yorodumi- PDB-5xvk: Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xvk | |||||||||
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Title | Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl Nicotinamide (MNA) | |||||||||
Components | Nicotinamide N-methyltransferase | |||||||||
Keywords | TRANSFERASE / NNMT / MNA / ternary complex / feedback inhibition / T2D | |||||||||
Function / homology | Function and homology information Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation ...Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Kannt, A. / Gosu, R. | |||||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / ...Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / Langer, T. / Rudolph, C. / Ruf, S. / Dhakshinamoorthy, S. / Gosu, R. / Kannt, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xvk.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xvk.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xvk_validation.pdf.gz | 984.6 KB | Display | wwPDB validaton report |
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Full document | 5xvk_full_validation.pdf.gz | 989.9 KB | Display | |
Data in XML | 5xvk_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5xvk_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/5xvk ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xvk | HTTPS FTP |
-Related structure data
Related structure data | 5xvqC 2i62S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31800.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nnmt / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O55239, nicotinamide N-methyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.27 Å3/Da / Density % sol: 41.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.25M Sodium thiocyanate, 22%(w/v) PEG 3350, 3% TMAO as additive |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→78.57 Å / Num. obs: 44282 / % possible obs: 99.7 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.536 / CC1/2: 0.869 / Rpim(I) all: 0.195 / Rrim(I) all: 0.572 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I62 Resolution: 1.88→78.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.937 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.134 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.06 Å2 / Biso mean: 15.41 Å2 / Biso min: 5.05 Å2
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Refinement step | Cycle: final / Resolution: 1.88→78.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.878→1.927 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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