+Open data
-Basic information
Entry | Database: PDB / ID: 2e5d | ||||||
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Title | Crystal structure of Human NMPRTase complexed with nicotinamide | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / NMPRTase / PBEF / Visfatin / PRTase | ||||||
Function / homology | Function and homology information nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell-cell signaling / cell junction / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Takahashi, R. / Nakamura, S. / Kobayashi, Y. / Ohkubo, T. | ||||||
Citation | Journal: J.Biochem. / Year: 2010 Title: Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase Authors: Takahashi, R. / Nakamura, S. / Nakazawa, T. / Minoura, K. / Yoshida, T. / Nishi, Y. / Kobayashi, Y. / Ohkubo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e5d.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e5d.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/2e5d ftp://data.pdbj.org/pub/pdb/validation_reports/e5/2e5d | HTTPS FTP |
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-Related structure data
Related structure data | 2e5bC 2e5cC 2h3bS C: citing same article (ref.) S: Starting model for refinement |
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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: 56378.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | #3: 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: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 38-40% pentaerythritol propoxylate (5/4 PO/OH), 50mM Tris-HCl, 200mM KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 71647 / % possible obs: 98.7 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.78 / Num. unique all: 4513 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H3B Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.566 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.152 / 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: 20.214 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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