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Yorodumi- PDB-4yde: CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yde | ||||||
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Title | CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE | ||||||
Components | (Protein farnesyltransferase/geranylgeranyltransferase type-1 ...) x 2 | ||||||
Keywords | TRANSFERASE / Farnesyl transferase | ||||||
Function / homology | Function and homology information Protein prenylyltransferase / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å | ||||||
Authors | Kumar, S. / Mabanglo, M.F. / Hast, M.A. / Shi, Y. / Beese, L.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE Authors: Kumar, S. / Mabanglo, M.F. / Hast, M.A. / Shi, Y. / 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 | 4yde.cif.gz | 314.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yde.ent.gz | 253.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/4yde ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4yde | HTTPS FTP |
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-Related structure data
Related structure data | 4l9pS 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/geranylgeranyltransferase type-1 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 39236.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: RAM2, CaO19.12280, CaO19.4817 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5APE8 |
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#2: Protein | Mass: 66693.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: RAM1, CaO19.12513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59LE1 |
-Non-polymers , 4 types, 154 molecules
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-4C7 / ( | #6: 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: 2.23 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 9%-13% PEG 2050 chips, 100 mM HEPES pH 7.2 100 -200 mM CaCl2, 5 uM ZnCl2 |
-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: Aug 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.82 Å / Num. obs: 26416 / % possible obs: 100 % / Redundancy: 14.5 % / Rsym value: 0.118 / Net I/σ(I): 31.1 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L9P Resolution: 2.701→47.822 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / 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: 2.701→47.822 Å
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Refine LS restraints |
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LS refinement shell |
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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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