+Open data
-Basic information
Entry | Database: PDB / ID: 2gvl | ||||||
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Title | Crystal Structure of Murine NMPRTase | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Visfatin / PBEF / NMPRTase / Cancer / FK866 | ||||||
Function / homology | Function and homology information regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity ...regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity / microglial cell activation / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / circadian rhythm / cell junction / nuclear speck / nucleotide binding / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Khan, J.A. / Tao, X. / Tong, L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents. Authors: Khan, J.A. / Tao, X. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gvl.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gvl.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/2gvl ftp://data.pdbj.org/pub/pdb/validation_reports/gv/2gvl | HTTPS FTP |
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-Related 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: 55568.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nampt / Production host: Escherichia coli (E. coli) References: UniProt: Q99KQ4, nicotinamide phosphoribosyltransferase #2: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.2 Details: 21% PEG3350 200mM NaCl Bacl2 as additive, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→82.76 Å / Num. all: 55602 / Num. obs: 55602 / % possible obs: 94.79 % / Observed criterion σ(I): 0.5 |
Reflection shell | Highest resolution: 2.1 Å / % possible all: 94.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→82.76 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.767 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.224 / 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: 21.314 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→82.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.153 Å / Total num. of bins used: 20
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