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Yorodumi- PDB-4ydo: CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ydo | ||||||
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Title | CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE IN APO FORM | ||||||
Components |
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Keywords | TRANSFERASE / Farnesyl transferase | ||||||
Function / homology | Function and homology information peptide pheromone maturation / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / protein geranylgeranylation Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 IN APO FORM 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 | 4ydo.cif.gz | 311 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ydo.ent.gz | 254.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ydo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/4ydo ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4ydo | HTTPS FTP |
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-Related structure data
Related structure data | 4ydeS 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: 39236.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: RAM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y765, protein farnesyltransferase, protein geranylgeranyltransferase type I | ||||
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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 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: RAM1, CaO19.12513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59LE1 | ||||
#3: Chemical | #4: Chemical | ChemComp-ZN / | #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: 2.15 Å3/Da / Density % sol: 42.8 % |
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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 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: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→52.82 Å / Num. obs: 18560 / % possible obs: 98.3 % / Redundancy: 7.97 % / Rsym value: 0.095 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.45 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YDE Resolution: 3→43.301 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.08 / 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: 3→43.301 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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