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Yorodumi- PDB-4l9p: Crystal structure of Aspergillus fumigatus protein farnesyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l9p | ||||||
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Title | Crystal structure of Aspergillus fumigatus protein farnesyltransferase complexed with the FII analog, FPT-II, and the KCVVM peptide | ||||||
Components |
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Keywords | TRANSFERASE / Ternary complex with isoprenoid and CAAX peptide substrate / CAAX farnesyltransferase / Isoprenoid and CAAX protein/peptide substrate | ||||||
Function / homology | Function and homology information peptide pheromone maturation / prenylation / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Mabanglo, M.F. / Hast, M.A. / Beese, L.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Authors: Mabanglo, M.F. / Hast, M.A. / Lubock, N.B. / Hellinga, H.W. / 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 | 4l9p.cif.gz | 372.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l9p.ent.gz | 297.5 KB | Display | PDB format |
PDBx/mmJSON format | 4l9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l9p ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l9p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-CaaX farnesyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 42391.461 Da / Num. of mol.: 1 / Mutation: N146S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: Af293 / Gene: AFUA_4G07800 / Plasmid: pCDF-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: Q4WP27, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Protein | Mass: 56635.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: Af293 / Gene: AFUA_4G10330 / Plasmid: pCDF-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q4WPS9, protein farnesyltransferase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 579.795 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 792 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ZN / | #7: Chemical | ChemComp-FII / [( | #8: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4-10% PEG6000, 600-800 mM LiCl, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2012 |
Radiation | Monochromator: Double-crystal, liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 156214 / Num. obs: 154808 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2 / % possible all: 82.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: > Homology model of A. fumigatus farnesyltransferase generated using PHYRE Resolution: 1.45→22.421 Å / SU ML: 0.12 / σ(F): 1.33 / Phase error: 13.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→22.421 Å
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Refine LS restraints |
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LS refinement shell |
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