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Yorodumi- PDB-3euv: Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3euv | ||||||
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Title | Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10, W102T, Y154T) in complex with BiotinGPP | ||||||
Components |
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Keywords | TRANSFERASE / protein prenylation / prenylome analysis / Prenyltransferase / Metal-binding / Phosphoprotein / Zinc | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / 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 / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / 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 / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / 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 / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / 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: 2.75 Å | ||||||
Authors | Guo, Z. / Nguyen, U.T.T. / Delon, C. / Bon, R.S. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H. / Wolters, D. / Alexandrov, K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2009 Title: Analysis of the eukaryotic prenylome by isoprenoid affinity tagging Authors: Nguyen, U.T.T. / Guo, Z. / Delon, C. / Wu, Y. / Deraeve, C. / Franzel, B. / Bon, R.S. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H. / Wolters, D. / Alexandrov, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3euv.cif.gz | 305.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3euv.ent.gz | 251.5 KB | Display | PDB format |
PDBx/mmJSON format | 3euv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3euv ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3euv | HTTPS FTP |
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-Related structure data
Related structure data | 3eu5C 1ft1S 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: 44098.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: coexpression of alpha-subunit from pGATEV and engineered beta-subunit from pET27b Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I |
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#2: Protein | Mass: 47602.168 Da / Num. of mol.: 1 Fragment: DELTA C-terminus 10 AA, RABGGTase BETA-subunit, UNP residues 1-427 Mutation: W102T, Y154T Source method: isolated from a genetically manipulated source Details: coexpression of alpha-subunit from pGATEV and engineered beta-subunit from pET27b Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-GBO / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 32179 / Num. obs: 32121 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 6.2 % / Biso Wilson estimate: 57 Å2 / Rsym value: 0.07 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 3247 / Rsym value: 0.353 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FT1 Resolution: 2.75→29.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.917 / SU B: 23.297 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.287 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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