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Yorodumi- PDB-2zir: Crystal Structure of rat protein farnesyltransferase complexed wi... -
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-Basic information
Entry | Database: PDB / ID: 2zir | ||||||
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Title | Crystal Structure of rat protein farnesyltransferase complexed with a benzofuran inhibitor and FPP | ||||||
Components | (Protein farnesyltransferase subunit ...) x 2 | ||||||
Keywords | TRANSFERASE / Prenyltransferase / Metal-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / : / positive regulation of cell cycle / response to cytokine / wound healing / response to organic cyclic compound / lipid metabolic process / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Fukami, T.A. / Sogabe, S. / Nagata, Y. / Kondoh, O. / Ishii, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Synthesis and structure-activity relationships of novel benzofuran farnesyltransferase inhibitors Authors: Asoh, K. / Kohchi, M. / Hyoudoh, I. / Ohtsuka, T. / Masubuchi, M. / Kawasaki, K. / Ebiike, H. / Shiratori, Y. / Fukami, T.A. / Kondoh, O. / Tsukaguchi, T. / Ishii, N. / Aoki, Y. / Shimma, N. / Sakaitani, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zir.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zir.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zir_validation.pdf.gz | 943.5 KB | Display | wwPDB validaton report |
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Full document | 2zir_full_validation.pdf.gz | 952.6 KB | Display | |
Data in XML | 2zir_validation.xml.gz | 32 KB | Display | |
Data in CIF | 2zir_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zir ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zir | HTTPS FTP |
-Related structure data
Related structure data | 2zisC 1fppS 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
-Protein farnesyltransferase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 44086.090 Da / Num. of mol.: 1 / Mutation: I156T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP / References: UniProt: Q04631, protein farnesyltransferase |
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#2: Protein | Mass: 49004.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP / References: UniProt: Q02293, protein farnesyltransferase |
-Non-polymers , 5 types, 405 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-FPP / | #6: Chemical | ChemComp-NH7 / | #7: 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: 3.2 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20mg/ml protein, 0.5mM FPP, 1mM inhibitor, 10% PEG6000, 0.2M Mg acetate, 0.1M Na acetate buffer, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 5, 2001 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→100 Å / Num. obs: 44027 / % possible obs: 95.9 % / Rmerge(I) obs: 0.045 / Χ2: 0.999 / Net I/σ(I): 21.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.333 / Cor.coef. Fo:Fc: 0.752
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 1FPP Resolution: 2.4→43 Å / FOM work R set: 0.837 / σ(F): 0
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Displacement parameters | Biso mean: 43.942 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 43
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Xplor file |
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