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Yorodumi- PDB-1tn7: Protein Farnesyltransferase Complexed with a TC21 Peptide Substra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tn7 | ||||||
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Title | Protein Farnesyltransferase Complexed with a TC21 Peptide Substrate and a FPP Analog at 2.3A Resolution | ||||||
Components |
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Keywords | TRANSFERASE / FTase / farnesyltransferase / farnesyl transferase / prenyltransferase / CaaX / TC21 / lipid modification / prenylation / substrate selectivity | ||||||
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 farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...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 farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / 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 / receptor tyrosine kinase binding / response to organic cyclic compound / 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: 2.3 Å | ||||||
Authors | Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity. Authors: Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tn7.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tn7.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/1tn7 ftp://data.pdbj.org/pub/pdb/validation_reports/tn/1tn7 | HTTPS FTP |
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-Related structure data
Related structure data | 1tn6C 1tn8C 1tnbC 1tnoC 1tnuC 1tnyC 1tnzC 1d8dS S: Starting model for refinement C: citing same article (ref.) |
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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 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04631, protein farnesyltransferase |
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#2: Protein | Mass: 48722.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02293, protein farnesyltransferase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1185.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the fusion protein was chemically synthesized |
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-Non-polymers , 4 types, 361 molecules
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-FII / [( | #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: 3.125 Å3/Da / Density % sol: 60.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 13% PEG 8000, 600 mM ammonium acetate pH 5.7, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2002 / Details: Bent cylindrical Si-mirror (Rh coating) |
Radiation | Monochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 52858 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5221 / Rsym value: 0.538 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1D8D Resolution: 2.3→25.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3564113.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.4099 Å2 / ksol: 0.380585 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→25.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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