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Yorodumi- PDB-3g8e: Crystal Structure of Rattus norvegicus Visfatin/PBEF/Nampt in Com... -
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-Basic information
Entry | Database: PDB / ID: 3g8e | ||||||
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Title | Crystal Structure of Rattus norvegicus Visfatin/PBEF/Nampt in Complex with an FK866-based inhibitor | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / PROTEIN-LIGAND COMPLEX / IS001 / Cytoplasm / Glycosyltransferase / Nucleus / Phosphoprotein / Pyridine nucleotide biosynthesis | ||||||
Function / homology | Function and homology information response to D-galactose / Nicotinamide salvaging / regulation of lung blood pressure / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / 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 / nicotinamide phosphoribosyltransferase activity / 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 / cellular response to ionizing radiation / female pregnancy / positive regulation of smooth muscle cell proliferation / microglial cell activation / 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: 3 Å | ||||||
Authors | Kang, G.B. / Bae, M.H. / Kim, M.K. / Im, I. / Kim, Y.C. / Eom, S.H. | ||||||
Citation | Journal: Mol.Cells / Year: 2009 Title: Crystal structure of Rattus norvegicus Visfatin/PBEF/Nampt in complex with an FK866-based inhibitor Authors: Kang, G.B. / Bae, M.H. / Kim, M.K. / Im, I. / Kim, Y.C. / 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 | 3g8e.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g8e.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 3g8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g8e_validation.pdf.gz | 828.7 KB | Display | wwPDB validaton report |
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Full document | 3g8e_full_validation.pdf.gz | 955 KB | Display | |
Data in XML | 3g8e_validation.xml.gz | 44 KB | Display | |
Data in CIF | 3g8e_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8e ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8e | HTTPS FTP |
-Related structure data
Related structure data | 2g95S 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: 55512.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: visfatin / Production host: Escherichia coli (E. coli) References: UniProt: Q80Z29, nicotinamide phosphoribosyltransferase #2: Chemical | |
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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: 49.21 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES-NaOH, 16% PEG 3350, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 22256 / Num. obs: 22256 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.14 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 8.25 / Rsym value: 0.334 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G95 Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å /
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