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Yorodumi- PDB-2g95: Crystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g95 | ||||||
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Title | Crystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor 1/Nicotinamide Phosphoribosyltransferase | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Visfatin / PBEF / NAmPRTase / Rattus norvegicus | ||||||
Function / homology | Function and homology information response to D-galactose / Nicotinamide salvaging / regulation of lung blood pressure / 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 ...response to D-galactose / Nicotinamide salvaging / regulation of lung blood pressure / 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 / female pregnancy / cellular response to ionizing radiation / microglial cell activation / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / response to organic cyclic compound / circadian rhythm / cellular response to amyloid-beta / cellular response to hypoxia / nucleotide binding / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kim, M.-K. / Eom, S.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structure of Visfatin/Pre-B Cell Colony-enhancing Factor 1/Nicotinamide Phosphoribosyltransferase, Free and in Complex with the Anti-cancer Agent FK-866 Authors: Kim, M.-K. / Lee, J.H. / Kim, H. / Park, S.J. / Kim, S.H. / Kang, G.B. / Lee, Y.S. / Kim, J.B. / Kim, K.K. / Suh, S.W. / Eom, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g95.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g95.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 2g95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/2g95 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g95 | 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: 55512.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pVFT / Production host: Escherichia coli (E. coli) References: UniProt: Q80Z29, 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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1M HEPES-NaOH at pH 7.2, 13-16% PEG3350, and 4-7% t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 80015 / Num. obs: 80015 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the Se-Met Phasing using other crystal Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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