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Yorodumi- PDB-1ft2: CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE COMPLEXED WIT... -
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-Basic information
Entry | Database: PDB / ID: 1ft2 | ||||||
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Title | CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYL DIPHOSPHATE SUBSTRATE | ||||||
Components | (PROTEIN FARNESYLTRANSFERASE) x 2 | ||||||
Keywords | TRANSFERASE / PROTEIN FARNESYLTRANSFERASE / FARNESYL DIPHOSPHATE / CANCER THERAPEUTICS / PRENYLTRANSFERASE / ISOPRENOID | ||||||
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 / MOLECULAR REPLACEMENT USING 1FT1 COORDINATES / Resolution: 3.4 Å | ||||||
Authors | Beese, L.S. / Casey, P.J. / Long, S.B. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Cocrystal structure of protein farnesyltransferase complexed with a farnesyl diphosphate substrate. Authors: Long, S.B. / Casey, P.J. / Beese, L.S. #1: Journal: Science / Year: 1997 Title: Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #2: Journal: Science / Year: 1997 Title: Erratum. Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #3: Journal: J.Biol.Chem. / Year: 1993 Title: High Level Expression of Mammalian Protein Farnesyltransferase in a Baculovirus System. The Purified Protein Contains Zinc Authors: Chen, W.J. / Moomaw, J.F. / Overton, L. / Kost, T.A. / Casey, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ft2.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ft2.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ft2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ft2_validation.pdf.gz | 637.8 KB | Display | wwPDB validaton report |
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Full document | 1ft2_full_validation.pdf.gz | 653.9 KB | Display | |
Data in XML | 1ft2_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 1ft2_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/1ft2 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/1ft2 | HTTPS FTP |
-Related structure data
Related structure data | 1ft1S 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: 38028.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Protein | Mass: 44829.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-FPP / |
Compound details | THIS PDB ENTRY CONTAINS THE COORDINATES OF A 3.4 ANGSTROM RESOLUTION CO-CRYSTAL STRUCTURE OF ...THIS PDB ENTRY CONTAINS THE COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 68 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP, PROTEIN CONCENTRATION OF 16MG/ML IN 20 MM KCL, 10UM ZNCL, 10MM DTT, 20MM TRIS PH 7.7, 0.12% OCTYL-BETA-D-GLUCOPYRANOSIDE, AND 1MM FARNESYL DIPHOSPHATE; RESERVOIR SOLUTION OF ...Details: HANGING DROP, PROTEIN CONCENTRATION OF 16MG/ML IN 20 MM KCL, 10UM ZNCL, 10MM DTT, 20MM TRIS PH 7.7, 0.12% OCTYL-BETA-D-GLUCOPYRANOSIDE, AND 1MM FARNESYL DIPHOSPHATE; RESERVOIR SOLUTION OF 15% PEG 8000, 200MM AMMONIUM ACETATE, PH 7.0, vapor diffusion - hanging drop PH range: 7.0-7.7 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 27, 1998 / Details: MSC DOUBLE-MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→35 Å / Num. obs: 17125 / % possible obs: 79.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3.4→3.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.199 / % possible all: 56.1 |
Reflection | *PLUS Num. measured all: 42609 |
Reflection shell | *PLUS % possible obs: 58.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT USING 1FT1 COORDINATES Starting model: PDB ENTRY 1FT1 Resolution: 3.4→35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITHOUT SUBSTRATE BOUND WAS DETERMINED TO 2.25 ANGSTROM RESOLUTION (APO FTASE, PDB ID CODE: 1FT1). PHASES FOR THE CO-CRYSTAL STRUCTURE OF ...Details: THE CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITHOUT SUBSTRATE BOUND WAS DETERMINED TO 2.25 ANGSTROM RESOLUTION (APO FTASE, PDB ID CODE: 1FT1). PHASES FOR THE CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITH FARNESYL DIPHOSPHATE BOUND WERE DERIVED FROM THIS HIGH RESOLUTION APO FTASE CRYSTAL STRUCTURE.
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Displacement parameters | Biso mean: 40.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 |